diff --git a/.coveragerc b/.coveragerc index 8db5982de..b2dfb82fe 100644 --- a/.coveragerc +++ b/.coveragerc @@ -1,5 +1,5 @@ [run] -omit = /usr/local/*,/home/travis/virtualenv/* +omit = /usr/local/*,/home/travis/virtualenv/*,*venv* [report] -omit = /usr/local/*,/home/travis/virtualenv/* +omit = */__init__.py, */test.py, */test_*.py diff --git a/.travis.yml b/.travis.yml index 9323e2edd..4688da240 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,6 +7,7 @@ before_install: - test/travis_before_install.sh install: - pip install -r backend/requirements.txt + - pip install -r test/requirements.txt - pip install coverage coveralls script: - test/travis_script.sh diff --git a/README.md b/README.md index 3a0bd11b3..e71807088 100644 --- a/README.md +++ b/README.md @@ -58,26 +58,15 @@ The application has only been tested with python 3.5.2. It will most likely work Quick development mode ---------------------- -1. Install docker (and docker-compose in case it's not included in the installation) -2. Create test database - - 1. Initiate a mysql data volume by running `./scripts/create_docker_db_volume_tarball.sh` or - `./scripts/download_and_create_docker_db_volume.sh` - - 2. Load mysql dummy data by running `./scripts/load_mysql_dummy_data.sh` - -3. Copy `settings_sample.json` into `settings.json` and - - Update the credentials for elixir and google oauth. - - Elixir/redirectUri: http://localhost:4000/elixir/login - - redirectUri: http://localhost:4000/login - - Set `mysqlHost` to `db` - - Set `mysqlSchema` to `swefreq_test` - - Clear `mysqlPasswd` (set it to empty `""`) -4. Make a symbolic link from `backend/static` to `static`. -5. Run the server: +1. Install docker (and docker-compose in case it's not included in the installation) +2. Run the server: ```bash $ docker-compose up ``` +3. Add test data to db: +```bash +$ psql -h localhost -U postgres swefreq -f test/data/browser_test_data.sql +``` [travis-badge]: https://travis-ci.org/NBISweden/swefreq.svg?branch=develop [travis-link]: https://travis-ci.org/NBISweden/swefreq diff --git a/backend/application.py b/backend/application.py index f67e57c61..8a3b7ca92 100644 --- a/backend/application.py +++ b/backend/application.py @@ -18,6 +18,7 @@ import db import handlers import settings +from modules.browser import utils def build_dataset_structure(dataset_version, user=None, dataset=None): @@ -60,7 +61,6 @@ class GetSchema(handlers.UnsafeHandler): figure out what information to return. """ def get(self): - dataset = None version = None try: @@ -137,16 +137,12 @@ def get(self): ret = [] if user: - futures = db.DatasetVersion.select( - ).join( - db.Dataset - ).join( - db.DatasetAccess - ).where( - db.DatasetVersion.available_from > datetime.now(), - db.DatasetAccess.user == user, - db.DatasetAccess.is_admin - ) + futures = (db.DatasetVersion.select() + .join(db.Dataset) + .join(db.DatasetAccess) + .where(db.DatasetVersion.available_from > datetime.now(), + db.DatasetAccess.user == user, + db.DatasetAccess.is_admin)) for f in futures: dataset = build_dataset_structure(f, user) dataset['future'] = True @@ -162,6 +158,7 @@ def get(self): class GetDataset(handlers.UnsafeHandler): def get(self, dataset, version=None): + dataset, version = utils.parse_dataset(dataset, version) user = self.current_user future_version = False @@ -182,6 +179,7 @@ def get(self, dataset, version=None): class ListDatasetVersions(handlers.UnsafeHandler): def get(self, dataset): + dataset, _ = utils.parse_dataset(dataset) user = self.current_user dataset = db.get_dataset(dataset) @@ -221,6 +219,7 @@ def get(self, dataset): class GenerateTemporaryLink(handlers.AuthorizedHandler): def post(self, dataset, version=None): + dataset, version = utils.parse_dataset(dataset, version) user = self.current_user dataset_version = db.get_dataset_version(dataset, version) if dataset_version is None: @@ -250,6 +249,7 @@ def post(self, dataset, version=None): class DatasetFiles(handlers.AuthorizedHandler): def get(self, dataset, version=None): + dataset, version = utils.parse_dataset(dataset, version) dataset_version = db.get_dataset_version(dataset, version) if dataset_version is None: self.send_error(status_code=404) @@ -272,6 +272,7 @@ def format_bytes(nbytes): class Collection(handlers.UnsafeHandler): def get(self, dataset): + dataset, _ = utils.parse_dataset(dataset) dataset = db.get_dataset(dataset) collections = {} @@ -376,6 +377,7 @@ def country_list(self): class RequestAccess(handlers.SafeHandler): def post(self, dataset): + dataset, _ = utils.parse_dataset(dataset) user = self.current_user dataset = db.get_dataset(dataset) @@ -408,6 +410,7 @@ def post(self, dataset): class LogEvent(handlers.SafeHandler): def post(self, dataset, event, target): + dataset, _ = utils.parse_dataset(dataset) user = self.current_user if event == 'consent': @@ -428,6 +431,7 @@ def post(self, dataset, event, target): class ApproveUser(handlers.AdminHandler): def post(self, dataset, email): + dataset, _ = utils.parse_dataset(dataset) with db.database.atomic(): dataset = db.get_dataset(dataset) @@ -470,6 +474,7 @@ def post(self, dataset, email): class RevokeUser(handlers.AdminHandler): def post(self, dataset, email): + dataset, _ = utils.parse_dataset(dataset) with db.database.atomic(): dataset = db.get_dataset(dataset) user = db.User.select().where(db.User.email == email).get() @@ -506,6 +511,7 @@ def _build_json_response(query, access_for): class DatasetUsersPending(handlers.AdminHandler): def get(self, dataset): + dataset, _ = utils.parse_dataset(dataset) dataset = db.get_dataset(dataset) users = db.User.select() access = (db.DatasetAccessPending @@ -520,6 +526,7 @@ def get(self, dataset): class DatasetUsersCurrent(handlers.AdminHandler): def get(self, dataset): + dataset, _ = utils.parse_dataset(dataset) dataset = db.get_dataset(dataset) users = db.User.select() access = (db.DatasetAccessCurrent @@ -563,6 +570,7 @@ def get(self): class ServeLogo(handlers.UnsafeHandler): def get(self, dataset): + dataset, _ = utils.parse_dataset(dataset) try: logo_entry = db.DatasetLogo.select( db.DatasetLogo diff --git a/backend/beacon.py b/backend/beacon.py index 50705a5ef..31c176d23 100644 --- a/backend/beacon.py +++ b/backend/beacon.py @@ -1,6 +1,6 @@ +import db import handlers -import pymongo -import settings + import tornado.web class Query(handlers.UnsafeHandler): @@ -65,6 +65,7 @@ def get(self): 'beacon': 'swefreq-beacon' }) + class Info(handlers.UnsafeHandler): def get(self): query_uri = "%s://%s/query?" % ('https', self.request.host) @@ -97,17 +98,11 @@ def get(self): ] # }) -def connect_mongo(dataset): - client = pymongo.MongoClient(host=settings.mongo_host, port=settings.mongo_port) - - auth_db = client['exac-user'] - auth_db.authenticate(settings.mongo_user, settings.mongo_password) - - return client[dataset] - def lookupAllele(chrom, pos, referenceAllele, allele, reference, dataset): #pylint: disable=too-many-arguments, unused-argument - """CHeck if an allele is present in the database + """ + Check if an allele is present in the database + Args: chrom: The chromosome, format matches [1-22XY] pos: Coordinate within a chromosome. Position is a number and is 0-based @@ -115,21 +110,26 @@ def lookupAllele(chrom, pos, referenceAllele, allele, reference, dataset): #pyli alternate: Any string of nucleotides A,C,T,G reference: The human reference build that was used dataset: Dataset to look in (currently used to select Mongo database) + Returns: The string 'true' if the allele was found, otherwise the string 'false' """ - if reference == 'hg19': - reference = 'GRChg37' - - dataset = "exac-{}-{}".format(dataset.lower(), reference) - - mdb = connect_mongo(dataset) - + # must add support for reference build # Beacon is 0-based, our database is 1-based in coords. + pos += 1 - res = mdb.variants.find({'chrom': chrom, 'pos': pos}) - for r in res: - if r['alt'] == allele and r['ref'] == referenceAllele: - return True - - return False + dataset_version = db.get_dataset_version(dataset) + if not dataset_version: + return None + try: + variant = (db.Variant + .select() + .where((db.Variant.pos == pos) & + (db.Variant.ref == referenceAllele) & + (db.Variant.alt == allele) & + (db.Variant.chrom == chrom) & + (db.Variant.dataset_version == dataset_version)) + .get()) + return True + except db.Variant.DoesNotExist: + return False diff --git a/backend/db.py b/backend/db.py index d3e329c3b..1ea48aa4c 100644 --- a/backend/db.py +++ b/backend/db.py @@ -1,5 +1,6 @@ #!/usr/bin/env python3 +import logging import settings from peewee import (BigIntegerField, BlobField, @@ -450,8 +451,11 @@ class Meta: def get_next_free_uid(): """ - Returns the next free uid >= 10000, and higher than the current uid's - from the sftp_user table in the database. + Get the next free uid >= 10000 and > than the current uids + from the sftp_user table in the db. + + Returns: + int: the next free uid """ default = 10000 next_uid = default @@ -464,27 +468,68 @@ def get_next_free_uid(): return next_uid + def get_admin_datasets(user): + """ + Get a list of datasets where user is admin + + Args: + user (User): Peewee User object for the user of interest + + Returns: + DataSetAccess: + """ return DatasetAccess.select().where( DatasetAccess.user == user, DatasetAccess.is_admin) -def get_dataset(dataset): + +def get_dataset(dataset:str): + """ + Given dataset name get Dataset + + Args: + dataset (str): short name of the dataset + + Returns: + Dataset: the corresponding DatasetVersion entry + """ dataset = Dataset.select().where( Dataset.short_name == dataset).get() return dataset -def get_dataset_version(dataset, version=None): + +def get_dataset_version(dataset:str, version:str=None): + """ + Given dataset get DatasetVersion + + Args: + dataset (str): short name of the dataset + + Returns: + DatasetVersion: the corresponding DatasetVersion entry + """ if version: - dataset_version = (DatasetVersion - .select(DatasetVersion, Dataset) - .join(Dataset) - .where(DatasetVersion.version == version, - Dataset.short_name == dataset)).get() + try: + dataset_version = (DatasetVersion + .select(DatasetVersion, Dataset) + .join(Dataset) + .where(DatasetVersion.version == version, + Dataset.short_name == dataset)).get() + except DatasetVersion.DoesNotExist: + logging.error("get_dataset_version({}, {}): ".format(dataset, version) + + "cannot retrieve dataset version") + return else: - dataset_version = (DatasetVersionCurrent - .select(DatasetVersionCurrent, Dataset) - .join(Dataset) - .where(Dataset.short_name == dataset)).get() + try: + dataset_version = (DatasetVersionCurrent + .select(DatasetVersionCurrent, Dataset) + .join(Dataset) + .where(Dataset.short_name == dataset)).get() + except DatasetVersionCurrent.DoesNotExist: + logging.error("get_dataset_version({}, version=None): ".format(dataset) + + "cannot retrieve dataset version") + return return dataset_version + def build_dict_from_row(row): d = {} diff --git a/backend/handlers.py b/backend/handlers.py index e832fa47b..4321081b1 100644 --- a/backend/handlers.py +++ b/backend/handlers.py @@ -13,7 +13,8 @@ class BaseHandler(tornado.web.RequestHandler): - """Base Handler. Handlers should not inherit from this + """ + Base Handler. Handlers should not inherit from this class directly but from either SafeHandler or UnsafeHandler to make security status explicit. """ @@ -66,7 +67,8 @@ def set_user_msg(self, msg, level="info"): self.set_cookie("msg", urllib.parse.quote( json_encode({"msg":msg, "level":level}) ) ) def write_error(self, status_code, **kwargs): - """ Overwrites write_error method to have custom error pages. + """ + Overwrites write_error method to have custom error pages. http://tornado.readthedocs.org/en/latest/web.html#tornado.web.RequestHandler.write_error """ logging.info("Error do something here again") @@ -102,11 +104,13 @@ class UnsafeHandler(BaseHandler): class SafeHandler(BaseHandler): - """ All handlers that need authentication and authorization should inherit + """ + All handlers that need authentication and authorization should inherit from this class. """ def prepare(self): - """This method is called before any other method. + """ + This method is called before any other method. Having the decorator @tornado.web.authenticated here implies that all the Handlers that inherit from this one are going to require authentication in all their methods. @@ -152,17 +156,18 @@ def prepare(self): class SafeStaticFileHandler(tornado.web.StaticFileHandler, SafeHandler): - """ Serve static files for logged in users """ - pass + Serve static files for logged in users + """ class BaseStaticNginxFileHandler(UnsafeHandler): - """Serve static files for users from the nginx frontend + """ + Serve static files for users from the nginx frontend Requires a ``path`` argument in constructor which should be the root of the nginx frontend where the files can be found. Then configure the nginx - frontend something like this + frontend something like this: :: location { internal; @@ -198,22 +203,21 @@ def get(self, dataset, file, user=None): class AuthorizedStaticNginxFileHandler(AuthorizedHandler, BaseStaticNginxFileHandler): - """Serve static files for authenticated users from the nginx frontend + """ + Serve static files for authenticated users from the nginx frontend - Requires a ``path`` argument in constructor which should be the root of + Requires a "path" argument in constructor which should be the root of the nginx frontend where the files can be found. Then configure the nginx - frontend something like this + frontend something like this: :: location { internal; alias ; } """ - pass class TemporaryStaticNginxFileHandler(BaseStaticNginxFileHandler): - def get(self, dataset, hash_value, file): logging.debug("Want to download hash {} ({})".format(hash_value, file)) linkhash = (db.Linkhash diff --git a/backend/modules/browser/browser_handlers.py b/backend/modules/browser/browser_handlers.py index 1d57f3988..58439f99a 100644 --- a/backend/modules/browser/browser_handlers.py +++ b/backend/modules/browser/browser_handlers.py @@ -1,169 +1,264 @@ +""" +Request handlers for the browser +""" + +import logging + +import db import handlers from . import lookups -from . import mongodb -from .utils import get_xpos, add_consequence_to_variant, remove_extraneous_vep_annotations, \ - order_vep_by_csq, get_proper_hgvs +from . import utils -class GetTranscript(handlers.UnsafeHandler): - def get(self, dataset, transcript): - transcript_id = transcript - ret = {'transcript':{}, - 'gene':{}, - } +class Autocomplete(handlers.UnsafeHandler): + def get(self, dataset:str, query:str, ds_version:str=None): + dataset, ds_version = utils.parse_dataset(dataset, ds_version) + ret = {} + + results = lookups.get_autocomplete(dataset, query, ds_version) + ret = {'values': sorted(list(set(results)))[:20]} + + self.finish(ret) - db_shared = mongodb.connect_db(dataset, True) - if not db_shared: - self.set_user_msg("Could not connect to database.", "error") - self.finish( ret ) + +class Download(handlers.UnsafeHandler): + def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): + """ + Download variants as csv + + Args: + dataset (str): dataset short name + datatype (str): type of data + item (str): query item + ds_version (str): dataset version + """ + dataset, ds_version = utils.parse_dataset(dataset, ds_version) + filename = "{}_{}_{}.csv".format(dataset, datatype, item) + self.set_header('Content-Type','text/csv') + self.set_header('content-Disposition','attachement; filename={}'.format(filename)) + + data = utils.get_variant_list(dataset, datatype, item, ds_version) + # Write header + self.write(','.join([h[1] for h in data['headers']]) + '\n') + + for variant in data['variants']: + headers = [h[0] for h in data['headers']] + self.write(','.join(map(str, [variant[h] for h in headers])) + '\n') + + +class GetCoverage(handlers.UnsafeHandler): + """ + Retrieve coverage + """ + def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): + dataset, ds_version = utils.parse_dataset(dataset, ds_version) + ret = utils.get_coverage(dataset, datatype, item, ds_version) + if 'region_too_large' in ret: + self.send_error(status_code=400, reason="The region is too large") + return + if not ret['coverage']: + self.send_error(status_code=404, reason="No coverage found") return + self.finish(ret) - # Add transcript information - transcript = lookups.get_transcript(db_shared, transcript_id) - ret['transcript']['id'] = transcript['transcript_id'] - ret['transcript']['number_of_CDS'] = len([t for t in transcript['exons'] if t['feature_type'] == 'CDS']) - # Add exon information +class GetCoveragePos(handlers.UnsafeHandler): + """ + Retrieve coverage range + """ + def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): + dataset, ds_version = utils.parse_dataset(dataset, ds_version) + ret = utils.get_coverage_pos(dataset, datatype, item, ds_version) + self.finish(ret) + + +class GetGene(handlers.UnsafeHandler): + """ + Request information about a gene + """ + def get(self, dataset:str, gene:str, ds_version:str=None): + """ + Request information about a gene + + Args: + dataset (str): short name of the dataset + gene (str): the gene id + """ + dataset, ds_version = utils.parse_dataset(dataset, ds_version) + gene_id = gene + + ret = {'gene':{'gene_id': gene_id}} + + # Gene + gene = lookups.get_gene(dataset, gene_id, ds_version) + if not gene: + self.send_error(status_code=404, reason='Gene not found') + ret['gene'] = gene + + # Add exons from transcript + transcript = lookups.get_transcript(dataset, gene['canonical_transcript'], ds_version) ret['exons'] = [] for exon in sorted(transcript['exons'], key=lambda k: k['start']): ret['exons'] += [{'start':exon['start'], 'stop':exon['stop'], 'type':exon['feature_type']}] - # Add gene information - gene = lookups.get_gene(db_shared, transcript['gene_id']) - ret['gene']['id'] = gene['gene_id'] - ret['gene']['name'] = gene['gene_name'] - ret['gene']['full_name'] = gene['full_gene_name'] - ret['gene']['canonical_transcript'] = gene['canonical_transcript'] + # Transcripts + transcripts_in_gene = lookups.get_transcripts_in_gene(dataset, gene_id, ds_version) + if transcripts_in_gene: + ret['transcripts'] = [] + for transcript in transcripts_in_gene: + ret['transcripts'] += [{'transcript_id':transcript['transcript_id']}] - gene_transcripts = lookups.get_transcripts_in_gene(db_shared, transcript['gene_id']) - ret['gene']['transcripts'] = [g['transcript_id'] for g in gene_transcripts] - self.finish( ret ) + # temporary fix for names + gene['gene_name'] = gene['name'] + gene['full_gene_name'] = gene['full_name'] + + self.finish(ret) class GetRegion(handlers.UnsafeHandler): - def get(self, dataset, region): - region = region.split('-') - REGION_LIMIT = 100000 - - chrom = region[0] - start = None - stop = None - if len(region) > 1: - start = int(region[1]) - if len(region) > 2: - stop = int(region[2]) - if not start: - start = 0 - if not stop and start: - stop = start - if start == stop: - start -= min(start, 20) - stop += 20 + """ + Request information about genes in a region + """ + def get(self, dataset:str, region:str, ds_version:str=None): + """ + Request information about genes in a region + + Args: + dataset (str): short name of the dataset + region (str): the region in the format chr-startpos-endpos + + Returns: + dict: information about the region and the genes found there + """ + dataset, ds_version = utils.parse_dataset(dataset, ds_version) + try: + chrom, start, stop = region.split('-') + start = int(start) + stop = int(stop) + except ValueError: + logging.error('GetRegion: unable to parse region ({})'.format(region)) + self.send_error(status_code=400, reason='Unable to parse region') + return + ret = {'region':{'chrom': chrom, 'start': start, 'stop': stop, - 'limit': REGION_LIMIT, }, } - db_shared = mongodb.connect_db(dataset, True) - if not db_shared: - self.set_user_msg("Could not connect to database.", "error") - self.finish( ret ) + if utils.is_region_too_large(start, stop): + self.send_error(status_code=400, reason="The region is too large") return - genes_in_region = lookups.get_genes_in_region(db_shared, chrom, start, stop) + genes_in_region = lookups.get_genes_in_region(dataset, chrom, start, stop, ds_version) if genes_in_region: ret['region']['genes'] = [] for gene in genes_in_region: ret['region']['genes'] += [{'gene_id':gene['gene_id'], - 'gene_name':gene['gene_name'], - 'full_gene_name':gene['full_gene_name'], + 'gene_name':gene['name'], + 'full_gene_name':gene['full_name'], }] - - self.finish( ret ) + self.finish(ret) -class GetGene(handlers.UnsafeHandler): - def get(self, dataset, gene): - gene_id = gene +class GetTranscript(handlers.UnsafeHandler): + """ + Request information about a transcript + """ + def get(self, dataset:str, transcript:str, ds_version:str=None): + """ + Request information about a transcript + + Args: + dataset (str): short name of the dataset + transcript (str): the transcript id + + Returns: + dict: transcript (transcript and exons), gene (gene information) + """ + dataset, ds_version = utils.parse_dataset(dataset, ds_version) + transcript_id = transcript + ret = {'transcript':{}, + 'gene':{}, + } - ret = {'gene':{'gene_id': gene_id}} - db = mongodb.connect_db(dataset, False) - db_shared = mongodb.connect_db(dataset, True) - if not db_shared or not db: - self.set_user_msg("Could not connect to database.", "error") - self.finish( ret ) + # Add transcript information + transcript = lookups.get_transcript(dataset, transcript_id, ds_version) + if not transcript: + self.send_error(status_code=404, reason='Transcript not found') return + ret['transcript']['id'] = transcript['transcript_id'] + ret['transcript']['number_of_CDS'] = len([t for t in transcript['exons'] if t['feature_type'] == 'CDS']) - # Gene - gene = lookups.get_gene(db_shared, gene_id) - ret['gene'] = gene - - # Add exons from transcript - transcript = lookups.get_transcript(db_shared, gene['canonical_transcript']) + # Add exon information ret['exons'] = [] for exon in sorted(transcript['exons'], key=lambda k: k['start']): ret['exons'] += [{'start':exon['start'], 'stop':exon['stop'], 'type':exon['feature_type']}] - # Variants - ret['gene']['variants'] = lookups.get_number_of_variants_in_transcript(db, gene['canonical_transcript']) + # Add gene information + gene = lookups.get_gene_by_dbid(transcript['gene']) + ret['gene']['id'] = gene['gene_id'] + ret['gene']['name'] = gene['name'] + ret['gene']['full_name'] = gene['full_name'] + ret['gene']['canonical_transcript'] = gene['canonical_transcript'] - # Transcripts - transcripts_in_gene = lookups.get_transcripts_in_gene(db_shared, gene_id) - if transcripts_in_gene: - ret['transcripts'] = [] - for transcript in transcripts_in_gene: - ret['transcripts'] += [{'transcript_id':transcript['transcript_id']}] + gene_transcripts = lookups.get_transcripts_in_gene_by_dbid(transcript['gene']) + ret['gene']['transcripts'] = [g['transcript_id'] for g in gene_transcripts] - self.finish( ret ) + self.finish(ret) class GetVariant(handlers.UnsafeHandler): - def get(self, dataset, variant): + """ + Request information about a gene + """ + def get(self, dataset:str, variant:str, ds_version:str=None): + """ + Request information about a gene + + Args: + dataset (str): short name of the dataset + variant (str): variant in the format chrom-pos-ref-alt + """ + dataset, ds_version = utils.parse_dataset(dataset, ds_version) ret = {'variant':{}} - - db = mongodb.connect_db(dataset, False) - db_shared = mongodb.connect_db(dataset, True) - - if not db_shared or not db: - self.set_user_msg("Could not connect to database.", "error") - self.finish( ret ) - return - # Variant v = variant.split('-') - variant = lookups.get_variant(db, db_shared, get_xpos(v[0], int(v[1])), v[2], v[3]) + try: + v[1] = int(v[1]) + except ValueError: + logging.error('GetVariant: unable to parse variant ({})'.format(variant)) + self.send_error(status_code=400, reason="Unable to parse variant") + return + orig_variant = variant + variant = lookups.get_variant(dataset, v[1], v[0], v[2], v[3], ds_version) - if variant is None: - variant = { - 'chrom': v[0], - 'pos': int(v[1]), - 'xpos': get_xpos(v[0], int(v[1])), - 'ref': v[2], - 'alt': v[3] - } + if not variant: + logging.error('Variant not found ({})'.format(orig_variant)) + self.send_error(status_code=404, reason='Variant not found') + return # Just get the information we need - for item in ["variant_id", "chrom", "pos", "ref", "alt", "filter", "rsid", "allele_num", + for item in ["variant_id", "chrom", "pos", "ref", "alt", "rsid", "allele_num", "allele_freq", "allele_count", "orig_alt_alleles", "site_quality", "quality_metrics", "transcripts", "genes"]: ret['variant'][item] = variant[item] + ret['variant']['filter'] = variant['filter_string'] # Variant Effect Predictor (VEP) annotations # https://www.ensembl.org/info/docs/tools/vep/vep_formats.html ret['variant']['consequences'] = [] if 'vep_annotations' in variant: - add_consequence_to_variant(variant) - variant['vep_annotations'] = remove_extraneous_vep_annotations(variant['vep_annotations']) + utils.add_consequence_to_variant(variant) + variant['vep_annotations'] = utils.remove_extraneous_vep_annotations(variant['vep_annotations']) # Adds major_consequence - variant['vep_annotations'] = order_vep_by_csq(variant['vep_annotations']) + variant['vep_annotations'] = utils.order_vep_by_csq(variant['vep_annotations']) ret['variant']['annotations'] = {} for annotation in variant['vep_annotations']: - annotation['HGVS'] = get_proper_hgvs(annotation) + annotation['HGVS'] = utils.get_proper_hgvs(annotation) # Add consequence type to the annotations if it doesn't exist consequence_type = annotation['Consequence'].split('&')[0] \ @@ -185,8 +280,19 @@ def get(self, dataset, variant): # Dataset frequencies. # This is reported per variable in the database data, with dataset - # information inside the variables, so here we reorder to make the + # information inside the variables, so here we reorder to make the # data easier to use in the template + + # get the variant for other datasets with the same reference_set + curr_dsv = db.get_dataset_version(dataset, ds_version) + dsvs = [db.get_dataset_version(dset.short_name) for dset in db.Dataset.select() if dset.short_name != dataset] + dsvs = [dsv for dsv in dsvs if dsv.reference_set == curr_dsv.reference_set] + dsv_groups = [(curr_dsv, variant)] + for dsv in dsvs: + hit = lookups.get_variant(dsv.dataset.short_name, v[1], v[0], v[2], v[3], dsv.version) + if hit: + dsv_groups.append((dsv, hit)) + frequencies = {'headers':[['Population','pop'], ['Allele Count','acs'], ['Allele Number', 'ans'], @@ -194,62 +300,76 @@ def get(self, dataset, variant): ['Allele Frequency', 'freq']], 'datasets':{}, 'total':{}} - for item in ['ans', 'acs', 'freq', 'homs']: - key = 'pop_' + item - if key not in variant: - continue - for _dataset, value in variant[key].items(): - if _dataset not in frequencies['datasets']: - frequencies['datasets'][_dataset] = {'pop':_dataset} - frequencies['datasets'][_dataset][item] = value - if item not in frequencies['total']: - frequencies['total'][item] = 0 - frequencies['total'][item] += value - if 'freq' in frequencies['total']: - frequencies['total']['freq'] /= len(frequencies['datasets'].keys()) - + term_map = {'allele_num':'ans', 'allele_count':'acs', 'allele_freq':'freq', 'hom_count':'homs'} + + for dsv_group in dsv_groups: + ds_name = dsv_group[0].dataset.short_name + + if ds_name not in frequencies['datasets']: + frequencies['datasets'][ds_name] = {'pop': ds_name} + for item in term_map: + if term_map[item] not in frequencies['total']: + frequencies['total'][term_map[item]] = 0 + if dsv_group[1][item] is None: + frequencies['datasets'][ds_name][term_map[item]] = 0 + else: + frequencies['datasets'][ds_name][term_map[item]] = dsv_group[1][item] + frequencies['total'][term_map[item]] += dsv_group[1][item] + + if 'freq' in frequencies['total']: + frequencies['total']['freq'] = frequencies['total']['acs']/frequencies['total']['ans'] ret['variant']['pop_freq'] = frequencies - self.finish( ret ) + self.finish(ret) class GetVariants(handlers.UnsafeHandler): - def get(self, dataset, datatype, item): - ret = mongodb.get_variant_list(dataset, datatype, item) + """ + Retrieve variants + """ + def get(self, dataset:str, datatype:str, item:str, ds_version:str=None): + """ + Retrieve variants + + Args: + dataset (str): short name of the dataset + datatype (str): gene, region, or transcript + item (str): item to query + """ + dataset, ds_version = utils.parse_dataset(dataset, ds_version) + ret = utils.get_variant_list(dataset, datatype, item, ds_version) + if not ret: + self.send_error(status_code=500, reason='Unable to retrieve variants') + return + if 'region_too_large' in ret: + self.send_error(status_code=400, reason="The region is too large") + return + # inconvenient way of doing humpBack-conversion headers = [] for a, h in ret['headers']: n = a[0] + "".join([b[0].upper() + b[1:] for b in a.split("_")])[1:] headers += [[n, h]] ret['headers'] = headers - self.finish( ret ) - - -class GetCoverage(handlers.UnsafeHandler): - def get(self, dataset, datatype, item): - ret = mongodb.get_coverage(dataset, datatype, item) - self.finish( ret ) - - -class GetCoveragePos(handlers.UnsafeHandler): - def get(self, dataset, datatype, item): - ret = mongodb.get_coverage_pos(dataset, datatype, item) - self.finish( ret ) + self.finish(ret) class Search(handlers.UnsafeHandler): - def get(self, dataset, query): + """ + Perform a search for the wanted object + """ + def get(self, dataset:str, query:str, ds_version:str=None): + """ + Perform a search for the wanted object + + Args: + dataset (str): short name of the dataset + query (str): search query + """ + dataset, ds_version = utils.parse_dataset(dataset, ds_version) ret = {"dataset": dataset, "value": None, "type": None} - db = mongodb.connect_db(dataset, False) - db_shared = mongodb.connect_db(dataset, True) - - if not db_shared or not db: - self.set_user_msg("Could not connect to database.", "error") - self.finish( ret ) - return - - datatype, identifier = lookups.get_awesomebar_result(db, db_shared, query) + datatype, identifier = lookups.get_awesomebar_result(dataset, query, ds_version) if datatype == "dbsnp_variant_set": datatype = "dbsnp" @@ -257,29 +377,4 @@ def get(self, dataset, query): ret["type"] = datatype ret["value"] = identifier - self.finish( ret ) - - -class Autocomplete(handlers.UnsafeHandler): - def get(self, dataset, query): - ret = {} - - results = mongodb.get_autocomplete(dataset, query) - ret = {'values': sorted(list(set(results)))[:20]} - - self.finish( ret ) - - -class Download(handlers.UnsafeHandler): - def get(self, dataset, datatype, item): - filename = "{}_{}_{}.csv".format(dataset, datatype, item) - self.set_header('Content-Type','text/csv') - self.set_header('content-Disposition','attachement; filename={}'.format(filename)) - - data = mongodb.get_variant_list(dataset, datatype, item) - # Write header - self.write(','.join([h[1] for h in data['headers']]) + '\n') - - for variant in data['variants']: - headers = [h[0] for h in data['headers']] - self.write(','.join(map(str, [variant[h] for h in headers])) + '\n') + self.finish(ret) diff --git a/backend/modules/browser/lookups.py b/backend/modules/browser/lookups.py index 829dff050..2539c824f 100644 --- a/backend/modules/browser/lookups.py +++ b/backend/modules/browser/lookups.py @@ -1,148 +1,48 @@ +import logging import re -from .utils import METRICS, AF_BUCKETS, get_xpos, xpos_to_pos, add_consequence_to_variants, add_consequence_to_variant +import db SEARCH_LIMIT = 10000 -def get_gene(sdb, gene_id): - return sdb.genes.find_one({'gene_id': gene_id}, projection={'_id': False}) - - -def get_gene_by_name(sdb, gene_name): - # try gene_name field first - gene = sdb.genes.find_one({'gene_name': gene_name}, projection={'_id': False}) - if gene: - return gene - # if not, try gene['other_names'] - return sdb.genes.find_one({'other_names': gene_name}, projection={'_id': False}) - - -def get_transcript(sdb, transcript_id): - transcript = sdb.transcripts.find_one({'transcript_id': transcript_id}, projection={'_id': False}) - if not transcript: - return None - transcript['exons'] = get_exons_in_transcript(sdb, transcript_id) - return transcript - - -def get_raw_variant(db, xpos, ref, alt, get_id=False): - return db.variants.find_one({'xpos': xpos, 'ref': ref, 'alt': alt}, projection={'_id': get_id}) - - -def get_variant(db, sdb, xpos, ref, alt): - variant = get_raw_variant(db, xpos, ref, alt, False) - if variant is None or 'rsid' not in variant: - return variant - if variant['rsid'] == '.' or variant['rsid'] is None: - rsid = sdb.dbsnp.find_one({'xpos': xpos}) - if rsid: - variant['rsid'] = 'rs%s' % rsid['rsid'] - return variant - - -def add_rsid_to_variant(sdb, variant): - if variant['rsid'] == '.' or variant['rsid'] is None: - rsid = sdb.dbsnp.find_one({'xpos': variant['xpos']}) - if rsid: - variant['rsid'] = 'rs%s' % rsid['rsid'] +REGION_REGEX = re.compile(r'^\s*(\d+|X|Y|M|MT)\s*([-:]?)\s*(\d*)-?([\dACTG]*)-?([ACTG]*)') -def get_variants_by_rsid(db, rsid): - if not rsid.startswith('rs'): - return None - try: - int(rsid.lstrip('rs')) - except ValueError: - return None - variants = list(db.variants.find({'rsid': rsid}, projection={'_id': False})) - add_consequence_to_variants(variants) - return variants +def get_autocomplete(dataset:str, query:str, ds_version:str=None): + """ + Provide autocomplete suggestions based on the query + Args: + dataset (str): short name of dataset + query (str): the query to compare to the available gene names + ds_version (str): the dataset version -def get_variants_from_dbsnp(db,sdb, rsid): - if not rsid.startswith('rs'): - return None + Returns: + list: A list of genes names whose beginning matches the query + """ try: - rsid = int(rsid.lstrip('rs')) - except ValueError: + ref_set = db.get_dataset_version(dataset, ds_version).reference_set + except AttributeError: return None - position = sdb.dbsnp.find_one({'rsid': rsid}) - if position: - variants = list(db.variants.find({'xpos': {'$lte': position['xpos'], '$gte': position['xpos']}}, projection={'_id': False})) - if variants: - add_consequence_to_variants(variants) - return variants - return [] - - -def get_coverage_for_bases(db, xstart, xstop=None): - """ - Get the coverage for the list of bases given by xstart->xstop, inclusive - Returns list of coverage dicts - xstop can be None if just one base, but you'll still get back a list - """ - if xstop is None: - xstop = xstart - - coverages = { - doc['xpos']: doc for doc in db.base_coverage.find( - {'xpos': {'$gte': xstart, '$lte': xstop}}, - projection={'_id': False} - ) - } - ret = [] - # We only store every 10'th base in the db, so we have to make the checks - # only then. - for i in range(xstart-xstart%10, xstop+1, 10): - if i in coverages: - ret.append(coverages[i]) - else: - ret.append({'xpos': i, 'pos': xpos_to_pos(i)}) - for item in ret: - item['has_coverage'] = 'mean' in item - del item['xpos'] - return ret - + query = (db.Gene.select(db.Gene.name) + .where(((db.Gene.name.startswith(query)) & + (db.Gene.reference_set == ref_set)))) + gene_names = [str(gene.name) for gene in query] + return gene_names -def get_coverage_for_transcript(db, xstart, xstop=None): - """ - :param db: - :param genomic_coord_to_exon: - :param xstart: - :param xstop: - :return: +def get_awesomebar_result(dataset:str, query:str, ds_version:str=None): """ - coverage_array = get_coverage_for_bases(db, xstart, xstop) - # only return coverages that have coverage (if that makes any sense?) - # return coverage_array - covered = [c for c in coverage_array if c['has_coverage']] - for c in covered: - del c['has_coverage'] - return covered - - -def get_constraint_for_transcript(db, transcript): - return db.constraint.find_one({'transcript': transcript}, projection={'_id': False}) - - -def get_exons_cnvs(db, transcript_name): - return list(db.cnvs.find({'transcript': transcript_name}, projection={'_id': False})) - + Parse the search input -def get_cnvs(db, gene_name): - return list(db.cnvgenes.find({'gene': gene_name}, projection={'_id': False})) + Datatype is one of: + - 'gene' + - 'transcript' + - 'variant' + - 'dbsnp_variant_set' + - 'region' -REGION_REGEX = re.compile(r'^\s*(\d+|X|Y|M|MT)\s*([-:]?)\s*(\d*)-?([\dACTG]*)-?([ACTG]*)') - -def get_awesomebar_result(db,sdb, query): - """ - Similar to the above, but this is after a user types enter - We need to figure out what they meant - could be gene, variant, region - - Return tuple of (datatype, identifier) - Where datatype is one of 'gene', 'variant', or 'region' - And identifier is one of: + Identifier is one of: - ensembl ID for gene - variant ID string for variant (eg. 1-1000-A-T) - region ID string for region (eg. 1-1000-2000) @@ -152,18 +52,18 @@ def get_awesomebar_result(db,sdb, query): - if a gene symbol, return that gene's ensembl ID - if an RSID, return that variant's string + Args: + dataset (str): short name of dataset + query (str): the search query + ds_version (str): the dataset version - Finally, note that we don't return the whole object here - only it's identifier. - This could be important for performance later - + Returns: + tuple: (datatype, identifier) """ query = query.strip() # Parse Variant types - variant = get_variants_by_rsid(db, query.lower()) - if not variant: - variant = get_variants_from_dbsnp(db,sdb, query.lower()) - + variant = get_variants_by_rsid(dataset, query.lower(), ds_version=ds_version) if variant: if len(variant) == 1: retval = ('variant', variant[0]['variant_id']) @@ -171,23 +71,23 @@ def get_awesomebar_result(db,sdb, query): retval = ('dbsnp_variant_set', variant[0]['rsid']) return retval - gene = get_gene_by_name(sdb, query) + gene = get_gene_by_name(dataset, query) # From here out, all should be uppercase (gene, tx, region, variant_id) query = query.upper() if not gene: - gene = get_gene_by_name(sdb, query) + gene = get_gene_by_name(dataset, query) if gene: return 'gene', gene['gene_id'] # Ensembl formatted queries if query.startswith('ENS'): # Gene - gene = get_gene(sdb, query) + gene = get_gene(dataset, query) if gene: return 'gene', gene['gene_id'] # Transcript - transcript = get_transcript(sdb, query) + transcript = get_transcript(dataset, query) if transcript: return 'transcript', transcript['transcript_id'] @@ -208,107 +108,473 @@ def get_awesomebar_result(db,sdb, query): return 'not_found', query -def get_genes_in_region(sdb, chrom, start, stop): +def get_coverage_for_bases(dataset:str, chrom:str, start_pos:int, end_pos:int=None, ds_version:str=None): + """ + Get the coverage for the list of bases given by start_pos->end_pos, inclusive + + Args: + dataset (str): short name for the dataset + chrom (str): chromosome + start_pos (int): first position of interest + end_pos (int): last position of interest; if None it will be set to start_pos + ds_version (str): version of the dataset + + Returns: + list: coverage dicts for the region of interest. None if failed """ - Genes that overlap a region + dataset_version = db.get_dataset_version(dataset, ds_version) + if not dataset_version: + return [] + + if end_pos is None: + end_pos = start_pos + return [values for values in (db.Coverage + .select() + .where((db.Coverage.pos >= start_pos) & + (db.Coverage.pos <= end_pos) & + (db.Coverage.chrom == chrom) & + (db.Coverage.dataset_version == dataset_version.id)) + .dicts())] + + +def get_coverage_for_transcript(dataset:str, chrom:str, start_pos:int, end_pos:int=None, ds_version:str=None): """ - xstart = get_xpos(chrom, start) - xstop = get_xpos(chrom, stop) - genes = sdb.genes.find({ - 'xstart': {'$lte': xstop}, - 'xstop': {'$gte': xstart}, - }, projection={'_id': False}) - return list(genes) + Get the coverage for the list of bases given by start_pos->end_pos, inclusive + Args: + dataset (str): short name for the dataset + chrom (str): chromosome + start_pos (int): first position of interest + end_pos (int): last position of interest; if None it will be set to start_pos + ds_version (str): version of the dataset -def get_variants_in_region(db, sdb, chrom, start, stop): + Returns: + list: coverage dicts for the region of interest """ - Variants that overlap a region - Unclear if this will include CNVs - """ - xstart = get_xpos(chrom, start) - xstop = get_xpos(chrom, stop) - variants = list(db.variants.find({ - 'xpos': {'$lte': xstop, '$gte': xstart} - }, projection={'_id': False}, limit=SEARCH_LIMIT)) - add_consequence_to_variants(variants) - for variant in variants: - add_rsid_to_variant(sdb, variant) - remove_extraneous_information(variant) - return list(variants) + # Is this function still relevant with postgres? + # Only entries with reported cov are in database + coverage_array = get_coverage_for_bases(dataset, chrom, start_pos, end_pos, ds_version) + # only return coverages that have coverage (if that makes any sense?) + # return coverage_array + if not coverage_array: + return [] + covered = [c for c in coverage_array if c['mean']] + return covered + + +def get_exons_in_transcript(dataset:str, transcript_id:str, ds_version=None): + """ + Retrieve exons associated with the given transcript id + + Args: + dataset (str): short name of the dataset + transcript_id (str): the id of the transcript + ds_version (str): dataset version + + Returns: + list: dicts with values for each exon sorted by start position + """ + try: + ref_set = db.get_dataset_version(dataset, ds_version).reference_set + except AttributeError: + logging.info('get_exons_in_transcript({}, {}): unable to find dataset dbid'.format(dataset, transcript_id)) + return None + try: + transcript = (db.Transcript + .select() + .join(db.Gene) + .where((db.Transcript.transcript_id == transcript_id) & + (db.Gene.reference_set == ref_set)) + .get()) + except db.Transcript.DoesNotExist: + logging.info('get_exons_in_transcript({}, {}): unable to retrieve transcript'.format(dataset, transcript_id)) + return None + wanted_types = ('CDS', 'UTR', 'exon') + return sorted(list(db.Feature.select().where((db.Feature.transcript == transcript) & + (db.Feature.feature_type in wanted_types)).dicts()), + key=lambda k: k['start']) + + +def get_gene(dataset:str, gene_id:str, ds_version:str=None): + """ + Retrieve gene by gene id + Args: + dataset (str): short name of the dataset + gene_id (str): the id of the gene + ds_version (str): dataset version -def get_metrics(db, variant): - if 'allele_count' not in variant or variant['allele_num'] == 0: + Returns: + dict: values for the gene; None if not found + """ + try: + ref_set = db.get_dataset_version(dataset, ds_version).reference_set + except AttributeError: + return None + try: + return db.Gene.select().where((db.Gene.gene_id == gene_id) & + (db.Gene.reference_set == ref_set)).dicts().get() + except db.Gene.DoesNotExist: return None - metrics = {} - for metric in METRICS: - metrics[metric] = db.metrics.find_one({'metric': metric}, projection={'_id': False}) - - metric = None - if variant['allele_count'] == 1: - metric = 'singleton' - elif variant['allele_count'] == 2: - metric = 'doubleton' - else: - for af in AF_BUCKETS: - if float(variant['allele_count'])/variant['allele_num'] < af: - metric = af - break - if metric is not None: - metrics['Site Quality'] = db.metrics.find_one({'metric': 'binned_%s' % metric}, projection={'_id': False}) - return metrics - - -def remove_extraneous_information(variant): - #del variant['genotype_depths'] - #del variant['genotype_qualities'] - del variant['transcripts'] - del variant['genes'] - del variant['orig_alt_alleles'] - del variant['xpos'] - del variant['xstart'] - del variant['xstop'] - del variant['site_quality'] - del variant['vep_annotations'] - - -def get_variants_in_gene(db, sdb, gene_id): - variants = [] - for variant in db.variants.find({'genes': gene_id}, projection={'_id': False}): - variant['vep_annotations'] = [x for x in variant['vep_annotations'] if x['Gene'] == gene_id] - add_rsid_to_variant(sdb, variant) - add_consequence_to_variant(variant) - remove_extraneous_information(variant) - variants.append(variant) + + +def get_gene_by_dbid(gene_dbid:str): + """ + Retrieve gene by gene database id + + Args: + gene_dbid (str): the database id of the gene + + Returns: + dict: values for the gene; empty if not found + """ + try: + return db.Gene.select().where(db.Gene.id == gene_dbid).dicts().get() + except db.Gene.DoesNotExist: + return {} + except ValueError: + return {} + + +def get_gene_by_name(dataset:str, gene_name:str, ds_version=None): + """ + Retrieve gene by gene_name. + First checks gene_name, then other_names. + + Args: + dataset (str): short name of the dataset + gene_name (str): the id of the gene + ds_version (str): dataset version + + Returns: + dict: values for the gene; empty if not found + """ + try: + ref_set = db.get_dataset_version(dataset, ds_version).reference_set + except AttributeError: + return {} + try: + return (db.Gene.select() + .where((db.Gene.reference_set == ref_set) & + (db.Gene.name==gene_name)) + .dicts() + .get()) + except db.Gene.DoesNotExist: + try: + return (db.GeneOtherNames.select(db.Gene) + .join(db.Gene) + .where((db.GeneOtherNames.name == gene_name) & + (db.Gene.reference_set == ref_set)) + .dicts() + .get()) + except db.GeneOtherNames.DoesNotExist: + logging.error('get_gene_by_name({}, {}): unable to retrieve gene'.format(dataset, gene_name)) + return {} + + +def get_genes_in_region(dataset:str, chrom:str, start_pos:int, stop_pos:int, ds_version:str=None): + """ + Retrieve genes located within a region + + Args: + dataset (str): short name of the dataset + chrom (str): chromosome name + start_pos (int): start of region + stop_pos (int): end of region + ds_version (str): dataset version + + Returns: + dict: values for the gene; empty if not found + """ + try: + ref_set = db.get_dataset_version(dataset, ds_version).reference_set + except AttributeError: + return {} + + gene_query = db.Gene.select().where((db.Gene.reference_set == ref_set) & + (db.Gene.start <= stop_pos) & + (db.Gene.stop >= start_pos) & + (db.Gene.chrom == chrom)).dicts() + return [gene for gene in gene_query] + + +def get_raw_variant(dataset:str, pos:int, chrom:str, ref:str, alt:str, ds_version:str=None): + """ + Retrieve variant by position and change + + Args: + dataset (str): short name of the reference set + pos (int): position of the variant + chrom (str): name of the chromosome + ref (str): reference sequence + alt (str): variant sequence + ds_version (str): dataset version + + Returns: + dict: values for the variant; None if not found + """ + dataset_version = db.get_dataset_version(dataset, ds_version) + if not dataset_version: + return None + + try: + variant = (db.Variant + .select() + .where((db.Variant.pos == pos) & + (db.Variant.ref == ref) & + (db.Variant.alt == alt) & + (db.Variant.chrom == chrom) & + (db.Variant.dataset_version == dataset_version)) + .dicts() + .get()) + variant['genes'] = [gene['gene_id'] for gene in + db.VariantGenes.select(db.Gene.gene_id) + .join(db.Gene) + .where(db.VariantGenes.variant == variant['id']) + .dicts()] + variant['transcripts'] = [transcript['transcript_id'] for transcript in + db.VariantTranscripts.select(db.Transcript.transcript_id) + .join(db.Transcript) + .where(db.VariantTranscripts.variant == variant['id']) + .dicts()] + return variant + except db.Variant.DoesNotExist: + logging.error('get_raw_variant({}, {}, {}, {}, {}, {}): unable to retrieve variant' + .format(dataset, pos, chrom, ref, alt, dataset_version.id)) + return None + + +def get_transcript(dataset:str, transcript_id:str, ds_version:str=None): + """ + Retrieve transcript by transcript id + Also includes exons as ['exons'] + + Args: + dataset (str): short name of the dataset + transcript_id (str): the id of the transcript + ds_version (str): dataset version + + Returns: + dict: values for the transcript, including exons; None if not found + """ + try: + ref_set = db.get_dataset_version(dataset, ds_version).reference_set + except AttributeError: + return None + try: + transcript = (db.Transcript + .select(db.Transcript, db.Gene.gene_id) + .join(db.Gene) + .where((db.Transcript.transcript_id == transcript_id) & + (db.Gene.reference_set == ref_set)) + .dicts() + .get()) + transcript['exons'] = get_exons_in_transcript(dataset, transcript_id) + return transcript + except db.Transcript.DoesNotExist: + return None + + +def get_transcripts_in_gene(dataset:str, gene_id:str, ds_version:str=None): + """ + Get the transcripts associated with a gene + Args: + dataset (str): short name of the reference set + gene_id (str): id of the gene + ds_version (str): dataset version + Returns: + list: transcripts (dict) associated with the gene; empty if no hits + """ + try: + ref_set = db.get_dataset_version(dataset, ds_version).reference_set + except AttributeError: + logging.error('get_transcripts_in_gene({}, {}): unable to get referenceset dbid'.format(dataset, gene_id)) + return [] + try: + gene = db.Gene.select().where((db.Gene.reference_set == ref_set) & + (db.Gene.gene_id == gene_id)).dicts().get() + except db.Gene.DoesNotExist: + logging.error('get_transcripts_in_gene({}, {}): unable to retrieve gene'.format(dataset, gene_id)) + return [] + + return [transcript for transcript in db.Transcript.select().where(db.Transcript.gene == gene['id']).dicts()] + + +def get_transcripts_in_gene_by_dbid(gene_dbid:int): + """ + Get the transcripts associated with a gene + Args: + gene_dbid (int): database id of the gene + Returns: + list: transcripts (dict) associated with the gene; empty if no hits + """ + return [transcript for transcript in db.Transcript.select().where(db.Transcript.gene == gene_dbid).dicts()] + + +def get_variant(dataset:str, pos:int, chrom:str, ref:str, alt:str, ds_version:str=None): + """ + Retrieve variant by position and change + + Args: + dataset (str): short name of the dataset + pos (int): position of the variant + chrom (str): name of the chromosome + ref (str): reference sequence + alt (str): variant sequence + ds_version (str): version of the dataset + + Returns: + dict: values for the variant; None if not found + """ + variant = get_raw_variant(dataset, pos, chrom, ref, alt, ds_version) + variant = get_raw_variant(dataset, pos, chrom, ref, alt, ds_version) + if variant and 'rsid' in variant and variant['rsid'] and not str(variant['rsid']).startswith('rs'): + variant['rsid'] = 'rs{}'.format(variant['rsid']) + return variant + + +def get_variants_by_rsid(dataset:str, rsid:str, ds_version:str=None): + """ + Retrieve variants by their associated rsid + + Args: + dataset (str): short name of dataset + rsid (str): rsid of the variant (starting with rs) + ds_version (str): version of the dataset + + Returns: + list: variants as dict; no hits returns None + """ + dataset_version = db.get_dataset_version(dataset, ds_version) + if not dataset_version: + return None + + if not rsid.startswith('rs'): + logging.error('get_variants_by_rsid({}, {}): rsid not starting with rs'.format(dataset, rsid)) + return None + + try: + rsid = int(rsid.lstrip('rs')) + except ValueError: + logging.error('get_variants_by_rsid({}, {}): not an integer after rs'.format(dataset, rsid)) + return None + query = (db.Variant + .select() + .where((db.Variant.rsid == rsid) & + (db.Variant.dataset_version == dataset_version)) + .dicts()) + + variants = [variant for variant in query] return variants -def get_transcripts_in_gene(sdb, gene_id): - return list(sdb.transcripts.find({'gene_id': gene_id}, projection={'_id': False})) +def get_variants_in_gene(dataset:str, gene_id:str, ds_version:str=None): + """ + Retrieve variants present inside a gene + Args: + dataset (str): short name of the dataset + gene_id (str): id of the gene + ds_version (str): version of the dataset -def get_number_of_variants_in_transcript(db, transcript_id): - total = db.variants.count({'transcripts': transcript_id}) - filtered = db.variants.count({'transcripts': transcript_id, 'filter': 'PASS'}) - return {'filtered': filtered, 'total': total} + Returns: + list: values for the variants + """ + dataset_version = db.get_dataset_version(dataset, ds_version) + if not dataset_version: + return None + gene = get_gene(dataset, gene_id, ds_version) + variants = [variant for variant in db.Variant.select() + .join(db.VariantGenes) + .where((db.VariantGenes.gene == gene['id']) & + (db.Variant.dataset_version == dataset_version)).dicts()] + ##### remove when db is fixed + for variant in variants: + if not variant['hom_count']: + variant['hom_count'] = 0 + variant['filter'] = variant['filter_string'] + ##### -def get_variants_in_transcript(db, sdb, transcript_id): - variants = [] - for variant in db.variants.find({'transcripts': transcript_id}, projection={'_id': False}): - variant['vep_annotations'] = [x for x in variant['vep_annotations'] if x['Feature'] == transcript_id] - add_rsid_to_variant(sdb, variant) - add_consequence_to_variant(variant) - remove_extraneous_information(variant) - variants.append(variant) + for variant in variants: + if variant['rsid']: + variant['rsid'] = 'rs{}'.format(variant['rsid']) return variants -def get_exons_in_transcript(sdb, transcript_id): - # return sorted( - # [x for x in - # db.exons.find({'transcript_id': transcript_id}, projection={'_id': False}) - # if x['feature_type'] != 'exon'], - # key=lambda k: k['start']) - return sorted(list(sdb.exons.find({'transcript_id': transcript_id, 'feature_type': { "$in": ['CDS', 'UTR', 'exon'] }}, projection={'_id': False})), key=lambda k: k['start']) +def get_variants_in_region(dataset:str, chrom:str, start_pos:int, end_pos:int, ds_version:str=None): + """ + Variants that overlap a region + + Args: + dataset (str): short name of the dataset + chrom (str): name of the chromosom + start_pos (int): start of the region + end_pos (int): start of the region + ds_version (str): version of the dataset + + Returns: + list: variant dicts, None if no hits + """ + dataset_version = db.get_dataset_version(dataset, ds_version) + if not dataset_version: + return None + query = (db.Variant + .select() + .where((db.Variant.pos >= start_pos) & + (db.Variant.pos <= end_pos) & + (db.Variant.chrom == chrom) & + (db.Variant.dataset_version == dataset_version)) + .dicts()) + + variants = [variant for variant in query] + + ##### remove when db is fixed + for variant in variants: + if not variant['hom_count']: + variant['hom_count'] = 0 + variant['filter'] = variant['filter_string'] + ##### + + for variant in variants: + if variant['rsid']: + variant['rsid'] = 'rs{}'.format(variant['rsid']) + return variants + + +def get_variants_in_transcript(dataset:str, transcript_id:str, ds_version:str=None): + """ + Retrieve variants inside a transcript + + Args: + dataset (str): short name of the dataset + transcript_id (str): id of the transcript (ENST) + ds_version (str): version of the dataset + + Returns: + dict: values for the variant; None if not found + """ + dataset_version = db.get_dataset_version(dataset, ds_version) + + transcript = get_transcript(dataset, transcript_id, ds_version) + if not transcript: + return None + + variants = [variant for variant in db.Variant.select() + .join(db.VariantTranscripts) + .where((db.VariantTranscripts.transcript == transcript['id']) & + (db.Variant.dataset_version == dataset_version)) + .dicts()] + + ##### remove when db is fixed + for variant in variants: + if not variant['hom_count']: + variant['hom_count'] = 0 + variant['filter'] = variant['filter_string'] + ##### + + for variant in variants: + variant['vep_annotations'] = [anno for anno in variant['vep_annotations'] if anno['Feature'] == transcript_id] + if variant['rsid']: + variant['rsid'] = 'rs{}'.format(variant['rsid']) + return variants diff --git a/backend/modules/browser/mongodb.py b/backend/modules/browser/mongodb.py deleted file mode 100644 index 72b0adce8..000000000 --- a/backend/modules/browser/mongodb.py +++ /dev/null @@ -1,132 +0,0 @@ -import logging -import pymongo - -from . import settings -from . import lookups -from .utils import get_xpos - -EXON_PADDING = 50 - -def connect_db(dataset, use_shared_data=False): - """ - Connects to a specific database based on the values stored in settings for - a given dataset, and whether to use shared data or not. - """ - database = 'shared' if use_shared_data else 'db' - try: - client = pymongo.MongoClient(connect=False, host=settings.mongo_host, port=settings.mongo_port) - - auth_db = client['exac-user'] - auth_db.authenticate(settings.mongo_user, settings.mongo_password) - - db = client[settings.mongo_databases[dataset][database]] - - return db - except pymongo.errors.ServerSelectionTimeoutError: - logging.error("Failed to connect to database '{}' for dataset '{}'".format(database, dataset)) - return None - - -def get_autocomplete(dataset, query): - try: - db_shared = connect_db(dataset, True) - results = db_shared.genes.distinct("gene_name", {"gene_name": {'$regex': '^{}.*'.format(query), '$options': 'i'}}) - return results - except pymongo.errors.OperationFailure as e: - logging.error("PyMongo OperationFailure: {}".format(e)) - - -def get_variant_list(dataset, datatype, item): - headers = [['variant_id','Variant'], ['chrom','Chrom'], ['pos','Position'], - ['HGVS','Consequence'], ['filter','Filter'], ['major_consequence','Annotation'], - ['flags','Flags'], ['allele_count','Allele Count'], ['allele_num','Allele Number'], - ['hom_count','Number of Homozygous Alleles'], ['allele_freq','Allele Frequency']] - - try: - db = connect_db(dataset, False) - db_shared = connect_db(dataset, True) - - if datatype == 'gene': - variants = lookups.get_variants_in_gene(db, db_shared, item) - elif datatype == 'region': - chrom, start, stop = item.split('-') - variants = lookups.get_variants_in_region(db, db_shared, chrom, start, stop) - elif datatype == 'transcript': - variants = lookups.get_variants_in_transcript(db, db_shared, item) - - # Format output - def format_variant(variant): - if variant['rsid'] == '.': - variant['rsid'] = '' - - variant['major_consequence'] = (variant['major_consequence'].replace('_variant','') - .replace('_prime_', '\'') - .replace('_', ' ')) - - # This is so an array values turns into a comma separated string instead - return {k: ", ".join(v) if isinstance(v,list) else v for k, v in variant.items()} - variants = list(map(format_variant, variants)) - return {'variants': variants, 'headers': headers} - - except pymongo.errors.OperationFailure as e: - logging.error("PyMongo OperationFailure: {}".format(e)) - - # TODO We should return a http error code here. - - -def get_coverage(dataset, datatype, item): - ret = {'coverage':[]} - - db = connect_db(dataset, False) - db_shared = connect_db(dataset, True) - try: - if datatype == 'gene': - gene = lookups.get_gene(db_shared, item) - transcript = lookups.get_transcript(db_shared, gene['canonical_transcript']) - xstart = transcript['xstart'] - EXON_PADDING - xstop = transcript['xstop'] + EXON_PADDING - ret['coverage'] = lookups.get_coverage_for_transcript(db, xstart, xstop) - elif datatype == 'region': - chrom, start, stop = item.split('-') - xstart = get_xpos(chrom, int(start)) - xstop = get_xpos(chrom, int(stop)) - ret['coverage'] = lookups.get_coverage_for_bases(db, xstart, xstop) - elif datatype == 'transcript': - transcript = lookups.get_transcript(db_shared, item) - xstart = transcript['xstart'] - EXON_PADDING - xstop = transcript['xstop'] + EXON_PADDING - ret['coverage'] = lookups.get_coverage_for_transcript(db, xstart, xstop) - - except pymongo.errors.OperationFailure as e: - logging.error("PyMongo OperationFailure: {}".format(e)) - - return ret - - -def get_coverage_pos(dataset, datatype, item): - ret = {'start':None, 'stop':None, 'chrom':None} - - db_shared = connect_db(dataset, True) - try: - if datatype == 'gene': - gene = lookups.get_gene(db_shared, item) - transcript = lookups.get_transcript(db_shared, gene['canonical_transcript']) - elif datatype == 'transcript': - transcript = lookups.get_transcript(db_shared, item) - - if datatype == 'region': - chrom, start, stop = item.split('-') - start = int(start) - stop = int(stop) - else: - start = transcript['start'] - EXON_PADDING - stop = transcript['stop'] + EXON_PADDING - chrom = transcript['chrom'] - - ret['start'] = start - ret['stop'] = stop - ret['chrom'] = chrom - except pymongo.errors.OperationFailure as e: - logging.error("PyMongo OperationFailure: {}".format(e)) - - return ret diff --git a/backend/modules/browser/route.py b/backend/modules/browser/route.py index df6913617..350c74f30 100755 --- a/backend/modules/browser/route.py +++ b/backend/modules/browser/route.py @@ -1,14 +1,14 @@ from . import browser_handlers as handlers # Browser links -routes = [ (r"/api/datasets/(?P[^\/]+)/browser/gene/(?P[^\/]+)", handlers.GetGene), - (r"/api/datasets/(?P[^\/]+)/browser/region/(?P[^\/]+)", handlers.GetRegion), - (r"/api/datasets/(?P[^\/]+)/browser/transcript/(?P[^\/]+)", handlers.GetTranscript), - (r"/api/datasets/(?P[^\/]+)/browser/variant/(?P[^\/]+)", handlers.GetVariant), - (r"/api/datasets/(?P[^\/]+)/browser/variants/(?P[^\/]+)/(?P[^\/]+)", handlers.GetVariants), - (r"/api/datasets/(?P[^\/]+)/browser/coverage/(?P[^\/]+)/(?P[^\/]+)", handlers.GetCoverage), - (r"/api/datasets/(?P[^\/]+)/browser/coverage_pos/(?P[^\/]+)/(?P[^\/]+)", handlers.GetCoveragePos), - (r"/api/datasets/(?P[^\/]+)/browser/autocomplete/(?P[^\/]+)", handlers.Autocomplete), - (r"/api/datasets/(?P[^\/]+)/browser/search/(?P[^\/]+)", handlers.Search), - (r"/api/datasets/(?P[^\/]+)/browser/download/(?P[^\/]+)/(?P[^\/]+)", handlers.Download), +routes = [(r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/gene/(?P[^/]+)" , handlers.GetGene), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/region/(?P[^\/]+)", handlers.GetRegion), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/transcript/(?P[^/]+)", handlers.GetTranscript), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/variant/(?P[^/]+)", handlers.GetVariant), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/variants/(?P[^/]+)/(?P[^/]+)", handlers.GetVariants), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/coverage/(?P[^/]+)/(?P[^/]+)", handlers.GetCoverage), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/coverage_pos/(?P[^/]+)/(?P[^/]+)", handlers.GetCoveragePos), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/autocomplete/(?P[^/]+)", handlers.Autocomplete), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/search/(?P[^/]+)", handlers.Search), + (r"/api/datasets/(?P[^/]+)/(?:version/(?P[^/]+)/)?browser/download/(?P[^/]+)/(?P[^/]+)", handlers.Download), ] diff --git a/backend/modules/browser/settings.py b/backend/modules/browser/settings.py deleted file mode 100644 index 875a002bd..000000000 --- a/backend/modules/browser/settings.py +++ /dev/null @@ -1,16 +0,0 @@ -import json - -try: - json_settings_fh = open("settings.json") -except FileNotFoundError: - json_settings_fh = open("../settings.json") - -json_settings = json.load(json_settings_fh) -json_settings_fh.close() - -# Mongodb settings -mongo_host = json_settings["mongoHost"] -mongo_port = json_settings["mongoPort"] -mongo_user = json_settings["mongoUser"] -mongo_password = json_settings["mongoPassword"] -mongo_databases = json_settings["mongoDatabases"] diff --git a/backend/modules/browser/tests/.coveragerc b/backend/modules/browser/tests/.coveragerc new file mode 100644 index 000000000..cea6a995c --- /dev/null +++ b/backend/modules/browser/tests/.coveragerc @@ -0,0 +1,15 @@ +[run] +omit = + # omit anything in a .local directory anywhere + */tests/* + */__init__.py + */venv/* + */virtualenv/* + +[report] +omit = + # omit anything in a .local directory anywhere + */tests/* + */__init__.py + */venv/* + */virtualenv/* diff --git a/backend/modules/browser/tests/__init__.py b/backend/modules/browser/tests/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/backend/modules/browser/tests/test_browser_handlers.py b/backend/modules/browser/tests/test_browser_handlers.py new file mode 100644 index 000000000..bb10efe85 --- /dev/null +++ b/backend/modules/browser/tests/test_browser_handlers.py @@ -0,0 +1,238 @@ +""" +Test the browser handlers +""" + +import requests +import json + +BASE_URL="http://localhost:4000" + +def test_get_autocomplete(): + """ + Test GetAutocomplete.get() + """ + dataset = 'SweGen' + + query = 'PA' + response = requests.get('{}/api/datasets/{}/browser/autocomplete/{}'.format(BASE_URL, dataset, query)) + data = json.loads(response.text) + assert set(data["values"]) == set(["PABPC1P9", "PACSIN2", "PANX2", "PARP4P3", + "PARVB", "PARVG", "PATZ1", "PAXBP1", "PAXBP1-AS1"]) + + +def test_download(): + """ + Test Download.get() + """ + dataset = 'SweGen' + + data_type = 'transcript' + data_item = 'ENST00000438441' + response = requests.get('{}/api/datasets/{}/browser/download/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + assert len(response.text.split('\n')) == 180 + + +def test_get_coverage(): + """ + Test GetCoverage.get() + """ + dataset = 'SweGen' + + data_type = 'transcript' + data_item = 'ENST00000438441' + response = requests.get('{}/api/datasets/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + data = json.loads(response.text) + assert len(data['coverage']) == 144 + data_type = 'region' + data_item = '1-1-1000000' + response = requests.get('{}/api/datasets/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + assert response.status_code == 400 + data_item = '1-1-5' + response = requests.get('{}/api/datasets/{}/browser/coverage/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + assert response.status_code == 404 + + +def test_get_coverage_pos(): + """ + Test GetCoveragePos.get() + """ + dataset = 'SweGen' + data_type = 'region' + data_item = '22-100001-100101' + response = requests.get('{}/api/datasets/{}/browser/coverage_pos/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + cov_pos = json.loads(response.text) + assert cov_pos['start'] == 100001 + assert cov_pos['stop'] == 100101 + assert cov_pos['chrom'] == '22' + + +def test_get_gene(): + """ + Test GetGene.get() + """ + dataset = 'SweGen' + gene_id = 'ENSG00000015475' + response = requests.get('{}/api/datasets/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id)) + expected = {"name": "BID", "canonicalTranscript": "ENST00000317361", "chrom": "22", "strand": "-", "geneName": "BID"} + gene = json.loads(response.text) + + for value in expected: + assert gene['gene'][value] == expected[value] + assert len(gene['exons']) == 14 + assert len(gene['transcripts']) == 10 + + dataset = 'SweGen' + gene_id = 'ENSG00000015475' + response = requests.get('{}/api/datasets/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id)) + expected = {"name": "BID", "canonicalTranscript": "ENST00000317361", "chrom": "22", "strand": "-", "geneName": "BID"} + gene = json.loads(response.text) + + dataset = 'SweGen' + gene_id = 'BAD_GENE_ID' + response = requests.get('{}/api/datasets/{}/browser/gene/{}'.format(BASE_URL, dataset, gene_id)) + assert response.status_code == 404 + + +def test_get_region(): + """ + Test GetRegion.get() + """ + dataset = 'SweGen' + region_def = '22-46615715-46615880' + response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def)) + region = json.loads(response.text) + expected = {'region': {'chrom': '22', + 'start': 46615715, + 'stop': 46615880, + 'genes': [{'fullGeneName': 'peroxisome proliferator-activated receptor alpha', + 'geneId': 'ENSG00000186951', + 'geneName': 'PPARA'}]}} + assert region == expected + + region_def = '22-16364870-16366200' + response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def)) + region = json.loads(response.text) + expected = {'region': {'chrom': '22', + 'start': 16364870, + 'stop': 16366200, + 'genes': [{'geneId': 'ENSG00000231565', + 'geneName': 'NEK2P2', + 'fullGeneName': 'NEK2 pseudogene 2'}]}} + assert region == expected + + region_def = '22-46A1615715-46615880' + response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def)) + assert response.status_code == 400 + + region_def = '22-1-1000000' + response = requests.get('{}/api/datasets/{}/browser/region/{}'.format(BASE_URL, dataset, region_def)) + assert response.status_code == 400 + + +def test_get_transcript(): + """ + Test GetTranscript.get() + """ + dataset = 'SweGen' + transcript_id = 'ENST00000317361' + response = requests.get('{}/api/datasets/{}/browser/transcript/{}'.format(BASE_URL, dataset, transcript_id)) + transcript = json.loads(response.text) + assert transcript['gene']['id'] == 'ENSG00000015475' + assert len(transcript['exons']) == 14 + + dataset = 'SweGen' + transcript_id = 'BAD_TRANSCRIPT' + response = requests.get('{}/api/datasets/{}/browser/transcript/{}'.format(BASE_URL, dataset, transcript_id)) + assert response.status_code == 404 + + +def test_get_variant(): + """ + Test GetVariant.get() + """ + dataset = 'SweGen' + variant_id = '22-16080482-CAT-C' + response = requests.get('{}/api/datasets/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id)) + variant = json.loads(response.text) + assert variant['variant']['variantId'] == '22-16080482-CAT-C' + assert set(variant['variant']['genes']) == set(['ENSG00000229286', 'ENSG00000235265']) + assert len(variant['variant']['genes']) == len(['ENSG00000229286', 'ENSG00000235265']) + assert set(variant['variant']['transcripts']) == set(['ENST00000448070', 'ENST00000413156']) + assert len(variant['variant']['transcripts']) == len(['ENST00000448070', 'ENST00000413156']) + + variant_id = '22-16269941-G-C' + response = requests.get('{}/api/datasets/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id)) + variant = json.loads(response.text) + assert variant['variant']['variantId'] == '22-16269941-G-C' + assert set(variant['variant']['genes']) == set(['ENSG00000198062', 'ENSG00000236666']) + assert len(variant['variant']['genes']) == len(['ENSG00000198062', 'ENSG00000236666']) + assert set(variant['variant']['transcripts']) == set(['ENST00000452800', 'ENST00000343518', 'ENST00000422014']) + assert len(variant['variant']['transcripts']) == len(['ENST00000452800', 'ENST00000343518', 'ENST00000422014']) + + variant_id = '21-9411609-G-T' + version = '20161223' + response = requests.get('{}/api/datasets/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id)) + assert response.status_code == 404 + response = requests.get('{}/api/datasets/{}/version/{}/browser/variant/{}'.format(BASE_URL, dataset, version, variant_id)) + variant = json.loads(response.text) + assert variant['variant']['variantId'] == '21-9411609-G-T' + + variant_id = '22-94358sfsdfsdf52-T-C' + response = requests.get('{}/api/datasets/{}/browser/variant/{}'.format(BASE_URL, dataset, variant_id)) + assert response.status_code == 400 + + +def test_get_variants(): + """ + Test GetVariants.get() + """ + dataset = 'SweGen' + + data_type = 'gene' + data_item = 'ENSG00000231565' + response = requests.get('{}/api/datasets/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + data = json.loads(response.text) + assert len(data['variants']) == 178 + + data_type = 'region' + data_item = '22-16360000-16361200' + response = requests.get('{}/api/datasets/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + data = json.loads(response.text) + assert len(data['variants']) == 13 + + data_type = 'region' + data_item = '22-46615715-46715880' + response = requests.get('{}/api/datasets/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + assert response.status_code == 400 + + data_type = 'transcript' + data_item = 'ENST00000438441' + response = requests.get('{}/api/datasets/{}/browser/variants/{}/{}'.format(BASE_URL, dataset, data_type, data_item)) + data = json.loads(response.text) + assert len(data['variants']) == 178 + + +def test_search(): + """ + Test Search.get() + """ + dataset = 'SweGen' + + query = 'NF1P3' + response = requests.get('{}/api/datasets/{}/browser/search/{}'.format(BASE_URL, dataset, query)) + data = json.loads(response.text) + assert data['type'] == 'gene' + assert data['value'] == 'ENSG00000183249' + + query = 'rs142856307' + response = requests.get('{}/api/datasets/{}/browser/search/{}'.format(BASE_URL, dataset, query)) + data = json.loads(response.text) + assert data['type'] == 'dbsnp' + assert data['value'] == 142856307 + + query = '21-9411281-T-C' + version = '20161223' + response = requests.get('{}/api/datasets/{}/version/{}/browser/search/{}'.format(BASE_URL, dataset, version, query)) + data = json.loads(response.text) + assert data['type'] == 'variant' + assert data['value'] == '21-9411281-T-C' diff --git a/backend/modules/browser/tests/test_lookups.py b/backend/modules/browser/tests/test_lookups.py new file mode 100644 index 000000000..21a13f5c9 --- /dev/null +++ b/backend/modules/browser/tests/test_lookups.py @@ -0,0 +1,360 @@ +""" +Tests for the functions available in lookups.py +""" + +from .. import lookups + + +def test_get_autocomplete(): + """ + Test get_autocomplete() + """ + res = lookups.get_autocomplete('SweGen', 'PA') + expected = set(["PABPC1P9", "PACSIN2", "PANX2", "PARP4P3", + "PARVB", "PARVG", "PATZ1", "PAXBP1", "PAXBP1-AS1"]) + assert set(res) == expected + res = lookups.get_autocomplete('Bad_dataset', 'PA') + assert not res + + +def test_get_awesomebar_result(): + """ + Test get_awesomebar_result() + """ + result = lookups.get_awesomebar_result('SweGen', 'rs142856307') + assert result == ('dbsnp_variant_set', 142856307) + result = lookups.get_awesomebar_result('SweGen', 'rs783') + assert result == ('variant', '22-29461622-G-A') + result = lookups.get_awesomebar_result('SweGen', 'NF1P3') + assert result == ('gene', 'ENSG00000183249') + result = lookups.get_awesomebar_result('SweGen', 'ENSG00000183249') + assert result == ('gene', 'ENSG00000183249') + result = lookups.get_awesomebar_result('SweGen', 'ENST00000457709') + assert result == ('transcript', 'ENST00000457709') + result = lookups.get_awesomebar_result('SweGen', '22-46615715-46615880') + assert result == ('region', '22-46615715-46615880') + result = lookups.get_awesomebar_result('SweGen', 'CHR22:46615715-46615880') + assert result == ('region', '22-46615715-46615880') + result = lookups.get_awesomebar_result('SweGen', 'CHR22-29461622-G-A') + assert result == ('variant', '22-29461622-G-A') + result = lookups.get_awesomebar_result('SweGen', 'DOES_NOT_EXIST') + assert result == ('not_found', 'DOES_NOT_EXIST') + + +def test_get_coverage_for_bases(): + """ + Test get_coverage_for_bases() + """ + # normal + coverage = lookups.get_coverage_for_bases('SweGen', '22', 46546423, 46549652) + assert len(coverage) == 323 + expected = {'chrom': '22', 'coverage': [1.0, 1.0, 0.993, 0.91, 0.697, 0.426, 0.2, 0.009, 0.0], + 'dataset_version': 4, 'mean': 24.94, 'median': 24.0, 'pos': 46546430} + for val in expected: + assert coverage[0][val] == expected[val] + + assert len(lookups.get_coverage_for_bases('SweGen', '22', 46615715, 46615880)) == 17 + + # no end_pos + coverage = lookups.get_coverage_for_bases('SweGen', '22', 46546430) + expected = {'chrom': '22', 'coverage': [1.0, 1.0, 0.993, 0.91, 0.697, 0.426, 0.2, 0.009, 0.0], + 'dataset_version': 4, 'mean': 24.94, 'median': 24.0, 'pos': 46546430} + for val in expected: + assert coverage[0][val] == expected[val] + assert len(lookups.get_coverage_for_bases('SweGen', '22', 46615715, 46615880)) == 17 + + # no hits + coverage = lookups.get_coverage_for_bases('SweGen', '1', 55500283, 55500285) + assert not coverage + + # incorrect dataset + assert not lookups.get_coverage_for_bases('BAD_DATASET', '1', 55500283, 55500320) + + +def test_get_coverage_for_transcript(): + """ + Test get_coverage_for_transcript() + """ + # normal + coverage = lookups.get_coverage_for_transcript('SweGen', '22', 46546423, 46549652) + assert len(coverage) == 323 + expected = {'chrom': '22', 'coverage': [1.0, 1.0, 0.993, 0.91, 0.697, 0.426, 0.2, 0.009, 0.0], + 'dataset_version': 4, 'mean': 24.94, 'median': 24.0, 'pos': 46546430} + for val in expected: + assert coverage[0][val] == expected[val] + assert len(lookups.get_coverage_for_transcript('SweGen', '22', 46615715, 46615880)) == 17 + + # no end_pos + coverage = lookups.get_coverage_for_transcript('SweGen', '22', 46546430) + expected = {'chrom': '22', 'coverage': [1.0, 1.0, 0.993, 0.91, 0.697, 0.426, 0.2, 0.009, 0.0], + 'dataset_version': 4, 'mean': 24.94, 'median': 24.0, 'pos': 46546430} + for val in expected: + assert coverage[0][val] == expected[val] + assert len(lookups.get_coverage_for_transcript('SweGen', '22', 46615715, 46615880)) == 17 + + # no hits + coverage = lookups.get_coverage_for_transcript('SweGen', '1', 55500283, 55500285) + assert not coverage + + # incorrect dataset + assert not lookups.get_coverage_for_transcript('BAD_DATASET', '1', 55500283, 55500320) + + +def test_get_exons_in_transcript(): + """ + Test get_exons_in_transcript() + """ + result = lookups.get_exons_in_transcript('SweGen', 'ENST00000215855') + assert len(result) == 14 + + # bad dataset + result = lookups.get_exons_in_transcript('NO_DATASET', 'ENST00000215855') + assert not result + + # bad transcript + result = lookups.get_exons_in_transcript('SweGen', 'BAD_TRANSCRIPT') + assert not result + + +def test_get_gene(): + """ + Test get_gene() + """ + # normal entry + expected = {'gene_id': 'ENSG00000251940', + 'name': 'SNORA15', + 'full_name': None, + 'canonical_transcript': 'ENST00000516131', + 'chrom': '22', + 'start': 19237396, + 'stop': 19237489, + 'strand': '+'} + + result = lookups.get_gene('SweGen', 'ENSG00000251940') + for val in expected: + assert result[val] == expected[val] + + # non-existing gene + result = lookups.get_gene('SweGen', 'NOT_A_GENE') + assert not result + + # non-existing dataset + result = lookups.get_gene('NoDataset', 'ENSG00000223972') + assert not result + + +def test_get_gene_by_dbid(): + """ + Test get_gene_by_dbid() + """ + # normal entry + expected = {'gene_id': 'ENSG00000226444', + 'name': 'ACTR3BP6', + 'full_name': 'ACTR3B pseudogene 6', + 'canonical_transcript': 'ENST00000421366', + 'chrom': '22', + 'start': 16967410, + 'stop': 16969212, + 'strand': '+'} + gene = lookups.get_gene('SweGen', 'ENSG00000226444') + result = lookups.get_gene_by_dbid(gene['id']) + for val in expected: + assert result[val] == expected[val] + + # non-existing genes + result = lookups.get_gene_by_dbid('NOT_A_GENE') + assert not result + result = lookups.get_gene_by_dbid(-1) + assert not result + + +def test_get_gene_by_name(caplog): + """ + Test get_gene_by_name() + """ + # normal entry + expected = {'gene_id': 'ENSG00000226444', + 'name': 'ACTR3BP6', + 'full_name': 'ACTR3B pseudogene 6', + 'canonical_transcript': 'ENST00000421366', + 'chrom': '22', + 'start': 16967410, + 'stop': 16969212, + 'strand': '+'} + result = lookups.get_gene_by_name('SweGen', 'ACTR3BP6') + for val in expected: + assert result[val] == expected[val] + + # non-existing gene + result = lookups.get_gene_by_name('SweGen', 'NOT_A_GENE') + assert not result + assert caplog.messages[0] == 'get_gene_by_name(SweGen, NOT_A_GENE): unable to retrieve gene' + + # non-existing dataset + result = lookups.get_gene_by_name('NoDataset', 'ENSG00000223972') + assert not result + + # name in other_names + result = lookups.get_gene_by_name('SweGen', 'BCL8C') + print(result) + assert result['gene_id'] == 'ENSG00000223875' + + +def test_get_genes_in_region(): + """ + Test get_genes_in_region() + """ + # stop_pos missing in db, so needs to be updated when available + # normal + res = lookups.get_genes_in_region('SweGen', '22', 25595800, 25615800) + expected_ids = set(['ENSG00000100053', 'ENSG00000236641', 'ENSG00000244752']) + gene_ids = set(gene['gene_id'] for gene in res) + assert gene_ids == expected_ids + res = lookups.get_genes_in_region('SweGen', '22', 16364870, 16366200) + expected_ids = ['ENSG00000231565'] + assert [gene['gene_id'] for gene in res] == expected_ids + # bad dataset + res = lookups.get_genes_in_region('bad_dataset', '22', 25595800, 25615800) + # nothing found + res = lookups.get_genes_in_region('SweGen', '22', 25595800, 25595801) + assert not res + + +def test_get_transcript(): + """ + Test get_transcript() + """ + # normal entry + expected = {'transcript_id': 'ENST00000398242', + 'chrom': '22', + 'start': 16122720, + 'stop': 16123768, + 'strand': '+'} + + result = lookups.get_transcript('SweGen', 'ENST00000398242') + for val in expected: + assert result[val] == expected[val] + assert len(result['exons']) == 1 + + # non-existing + assert not lookups.get_transcript('SweGen', 'INCORRECT') + + +def test_get_transcripts_in_gene(): + """ + Test get_transcripts_in_gene() + """ + res = lookups.get_transcripts_in_gene('SweGen', 'ENSG00000228314') + assert len(res) == 3 + + assert not lookups.get_transcripts_in_gene('bad_dataset', 'ENSG00000241670') + assert not lookups.get_transcripts_in_gene('SweGen', 'ENSGASDFG') + + +def test_get_raw_variant(): + """ + Test get_raw_variant + """ + result = lookups.get_raw_variant('SweGen', 16080482, '22', 'CAT', 'C') + assert set(result['genes']) == set(['ENSG00000229286', 'ENSG00000235265']) + assert len(result['genes']) == len(['ENSG00000229286', 'ENSG00000235265']) + assert set(result['transcripts']) == set(['ENST00000448070', 'ENST00000413156']) + assert len(result['transcripts']) == len(['ENST00000448070', 'ENST00000413156']) + assert not lookups.get_raw_variant('SweGen', 55500281, '1', 'A', 'T') + assert not lookups.get_raw_variant('bad_dataset', 55500283, '1', 'A', 'T') + + +def test_get_transcripts_in_gene_by_dbid(): + """ + Test get_transcripts_in_gene_by_dbid() + """ + gene = lookups.get_gene('SweGen', 'ENSG00000228314') + res = lookups.get_transcripts_in_gene_by_dbid(gene['id']) + assert len(res) == 3 + res = lookups.get_transcripts_in_gene_by_dbid(-1) + assert not res + + +def test_get_variant(): + """ + Test get_variant() + """ + result = lookups.get_variant('SweGen', 16080482, '22', 'CAT', 'C') + assert result['variant_id'] == '22-16080482-CAT-C' + assert set(result['genes']) == set(['ENSG00000229286', 'ENSG00000235265']) + assert len(result['genes']) == len(['ENSG00000229286', 'ENSG00000235265']) + assert set(result['transcripts']) == set(['ENST00000448070', 'ENST00000413156']) + assert len(result['transcripts']) == len(['ENST00000448070', 'ENST00000413156']) + result = lookups.get_variant('SweGen', 9411609, '21', 'G', 'T') + assert not result + + # incorrect position + assert not lookups.get_variant('SweGen', -1, '1', 'A', 'T') + + # with version + result = lookups.get_variant('SweGen', 16057464, '22', 'G', 'A', "20161223") + assert not result + result = lookups.get_variant('SweGen', 9411609, '21', 'G', 'T', "20161223") + assert result['variant_id'] == '21-9411609-G-T' + + +def test_get_variants_by_rsid(): + ''' + Test get_variants_by_rsid() + ''' + # normal + result = lookups.get_variants_by_rsid('SweGen', 'rs142856307') + assert result[0]['pos'] == 16285954 + assert len(result) == 5 + assert not lookups.get_variants_by_rsid('SweGen', 'rs76676778') + # with version + assert not lookups.get_variants_by_rsid('SweGen', 'rs185758992', '20161223') + result = lookups.get_variants_by_rsid('SweGen', 'rs76676778', '20161223') + assert result[0]['variant_id'] == '21-9411609-G-T' + + # errors + assert lookups.get_variants_by_rsid('incorrect_name', 'rs373706802') is None + assert lookups.get_variants_by_rsid('SweGen', '373706802') is None + assert lookups.get_variants_by_rsid('SweGen', 'rs3737o68o2') is None + + # no variants with rsid available + assert not lookups.get_variants_by_rsid('SweGen', 'rs1') + + +def test_get_variants_in_gene(): + """ + Test get_variants_in_gene() + """ + res = lookups.get_variants_in_gene('SweGen', 'ENSG00000198062') + assert len(res) == 512 + assert not lookups.get_variants_in_gene('bad_dataset', 'ENSG00000198062') + assert not lookups.get_variants_in_gene('bad_dataset', 'ENSGASDFG') + assert not lookups.get_variants_in_gene('SweGen', 'ENSG00000198062', "BAD_VERSION") + + +def test_get_variants_in_region(): + """ + Test get_variants_in_region() + """ + # normal + result = lookups.get_variants_in_region('SweGen', '22', 16079200, 16079400) + expected_pos = [16079227, 16079289] + assert [res['pos'] for res in result] == expected_pos + + # no positions covered + result = lookups.get_variants_in_region('SweGen', '22', 16079200, 16079000) + assert not result + + # incorrect dataset + result = lookups.get_variants_in_region('Incorrect_dataset', '22', 16079200, 16079400) + assert not result + + +def test_get_variants_in_transcript(): + """ + Test get_variants_in_transcript() + """ + res = lookups.get_variants_in_transcript('SweGen', 'ENST00000452800') + assert len(res) == 508 + assert not lookups.get_variants_in_transcript('BAD_DATASET', 'ENST00000452800') + assert not lookups.get_variants_in_transcript('SweGen', 'ENST123') diff --git a/backend/modules/browser/tests/test_utils.py b/backend/modules/browser/tests/test_utils.py new file mode 100644 index 000000000..73c7501b9 --- /dev/null +++ b/backend/modules/browser/tests/test_utils.py @@ -0,0 +1,283 @@ +""" +Tests for utils.py +""" + +from .. import lookups +from .. import utils + + +def test_add_consequence_to_variants(): + """ + Test add_consequence_to_variants() + """ + variants = [] + variants.append(lookups.get_variant('SweGen', 16252949, '22', 'T', 'G')) + variants.append(lookups.get_variant('SweGen', 16269934, '22', 'A', 'G')) + + utils.add_consequence_to_variants(variants) + assert variants[0]['major_consequence'] == 'downstream_gene_variant' + assert variants[1]['major_consequence'] == 'missense_variant' + + +def test_add_consequence_to_variant(): + """ + Test add_consequence_to_variant() + """ + variant = lookups.get_variant('SweGen', 16252949, '22', 'T', 'G') + utils.add_consequence_to_variant(variant) + assert variant['major_consequence'] == 'downstream_gene_variant' + + variant['vep_annotations'][0]['Consequence'] = "stop_gained" + utils.add_consequence_to_variant(variant) + assert variant['category'] == 'lof_variant' + assert variant['major_consequence'] == 'stop_gained' + + variant = lookups.get_variant('SweGen', 16269985, '22', 'C', 'G') + utils.add_consequence_to_variant(variant) + assert variant['category'] == 'other_variant' + assert variant['major_consequence'] == 'intron_variant' + + variant = lookups.get_variant('SweGen', 16277852, '22', 'C', 'T') + utils.add_consequence_to_variant(variant) + assert variant['major_consequence'] == 'synonymous_variant' + assert variant['category'] == 'synonymous_variant' + + variant = lookups.get_variant('SweGen', 16269934, '22', 'A', 'G') + utils.add_consequence_to_variant(variant) + assert variant['category'] == 'missense_variant' + assert variant['major_consequence'] == 'missense_variant' + + variant['vep_annotations'] = [] + utils.add_consequence_to_variant(variant) + assert variant['major_consequence'] == '' + + # bad variant + variant = lookups.get_variant('SweGen', 38481311, '444', 'C', 'T') + utils.add_consequence_to_variant(variant) + assert not variant + + +def test_annotation_severity(): + """ + Test annotation_severity() + """ + variant = lookups.get_variant('SweGen', 16269934, '22', 'A', 'G') + res = utils.annotation_severity(variant['vep_annotations'][0]) + assert res == -26.9 + + +def test_get_coverage(): + """ + Test get_coverage() + """ + res = utils.get_coverage('SweGen', 'gene', 'ENSG00000231565') + assert len(res['coverage']) == 144 + res = utils.get_coverage('SweGen', 'region', '22-46615715-46615880') + assert len(res['coverage']) == 17 + res = utils.get_coverage('SweGen', 'region', '22:46615715-46615880') + assert not res['coverage'] + assert res['bad_region'] + res = utils.get_coverage('SweGen', 'region', '22-46615715asd-46615880') + assert not res['coverage'] + assert res['bad_region'] + res = utils.get_coverage('SweGen', 'transcript', 'ENST00000438441') + assert len(res['coverage']) == 144 + + assert not utils.get_coverage('BAD_SET', 'transcript', 'ENST00000438441')['coverage'] + + res = utils.get_coverage('SweGen', 'region', '22-1-1000000') + assert res['region_too_large'] + + +def test_get_coverage_pos(): + """ + Test get_coverage_pos() + """ + res = utils.get_coverage_pos('SweGen', 'gene', 'ENSG00000231565') + assert res['chrom'] == '22' + assert res['start'] == 16364817 + assert res['stop'] == 16366254 + res = utils.get_coverage_pos('SweGen', 'region', '22-46615715-46615880') + assert res['chrom'] == '22' + assert res['start'] == 46615715 + assert res['stop'] == 46615880 + res = utils.get_coverage_pos('SweGen', 'transcript', 'ENST00000438441') + assert res['chrom'] == '22' + assert res['start'] == 16364817 + assert res['stop'] == 16366254 + + res = utils.get_coverage_pos('BAD_SET', 'transcript', 'ENST00000438441') + for value in res.values(): + assert not value + + +def test_data_structures(): + """ + Test the constants + """ + assert len(utils.CSQ_ORDER) == len(set(utils.CSQ_ORDER)) # No duplicates + assert all(csq == utils.REV_CSQ_ORDER_DICT[utils.CSQ_ORDER_DICT[csq]] for csq in utils.CSQ_ORDER) + + +def test_get_flags_from_variant(): + """ + Test get_flags_from_variant() + """ + fake_variant = {'vep_annotations':[{'LoF': 'LC', 'LoF_flags': 'something'}, + {'LoF': '', 'LoF_flags': ''}, + {'LoF': 'LC', 'LoF_flags': 'something'}]} + flags = utils.get_flags_from_variant(fake_variant) + assert flags == ['LC LoF', 'LoF flag'] + + fake_variant = {'vep_annotations':[{'LoF': 'LC', 'LoF_flags': 'something'}, + {'LoF': 'HC', 'LoF_flags': 'something'}]} + flags = utils.get_flags_from_variant(fake_variant) + assert flags == ['LoF flag'] + + fake_variant = {'mnps': 'no idea', 'vep_annotations':[]} + flags = utils.get_flags_from_variant(fake_variant) + assert flags == ['MNP'] + + +def test_get_proper_hgvs(): + """ + Test get_proper_hgvs() + """ + annotation = {'HGVSc': 'ENST00000343518.6:c.35C>T', + 'HGVSp': 'ENSP00000340610.6:p.Ser12Phe', + 'major_consequence': 'splice_donor_variant'} + assert utils.get_proper_hgvs(annotation) == 'c.35C>T' + annotation['major_consequence'] = 'coding_sequence_variant' + assert utils.get_proper_hgvs(annotation) == 'p.Ser12Phe' + assert not utils.get_proper_hgvs(dict()) + + +def test_get_protein_hgvs(): + """ + Test get_protein_hgvs() + """ + annotation = {'HGVSc': 'ENST00000343518.6:c.35C>T', + 'HGVSp': 'ENSP00000340610.6:p.Ser12Phe'} + result = utils.get_protein_hgvs(annotation) + assert result == 'p.Ser12Phe' + annotation = {'HGVSc': 'ENST00000343518.6:c.27G>A', + 'HGVSp': 'ENST00000343518.6:c.27G>A(p.%3D)', + 'Protein_position': '9', + 'Amino_acids': 'P'} + result = utils.get_protein_hgvs(annotation) + assert result == 'p.Pro9Pro' + annotation['Amino_acids'] = 'Z' + assert not utils.get_protein_hgvs(annotation) + assert not utils.get_protein_hgvs(dict()) + + +def test_get_transcript_hgvs(): + """ + Test get_transcript_hgvs() + + """ + annotation = {'HGVSc': 'ENST00000343518.6:c.35C>T', + 'HGVSp': 'ENSP00000340610.6:p.Ser12Phe'} + assert utils.get_transcript_hgvs(annotation) == 'c.35C>T' + assert not utils.get_transcript_hgvs(dict()) + + +def test_get_variant_list(): + """ + Test get_variant_list() + """ + res = utils.get_variant_list('SweGen', 'gene', 'ENSG00000231565') + assert len(res['variants']) == 178 + res = utils.get_variant_list('SweGen', 'region', '22-16360000-16361200') + assert len(res['variants']) == 13 + res = utils.get_variant_list('SweGen', 'transcript', 'ENST00000438441') + assert len(res['variants']) == 178 + res = utils.get_variant_list('SweGen', 'transcript', 'ENSTWEIRD') + assert not res + res = utils.get_variant_list('SweGen', 'region', '22-1-1000000') + assert res['region_too_large'] + + res = utils.get_variant_list('SweGen', 'region', '22-11000000') + assert not res + + +def test_order_vep_by_csq(): + """ + Test order_vep_by_csq() + """ + annotation = [{'Consequence': 'frameshift_variant'}, + {'Consequence': 'transcript_ablation'}, + {'Consequence': 'mature_miRNA_variant'}] + expected = [{'Consequence': 'transcript_ablation', + 'major_consequence': 'transcript_ablation'}, + {'Consequence': 'frameshift_variant', + 'major_consequence': 'frameshift_variant'}, + {'Consequence': 'mature_miRNA_variant', + 'major_consequence': 'mature_miRNA_variant'}] + result = utils.order_vep_by_csq(annotation) + assert result == expected + assert utils.order_vep_by_csq([dict()]) == [{'major_consequence': ''}] + + +def test_parse_dataset(): + assert utils.parse_dataset('SweGen') == ('SweGen', None) + assert utils.parse_dataset('SweGen', '180101') == ('SweGen', '180101') + assert utils.parse_dataset('hg19:SweGen:180101') == ('SweGen', '180101') + + +def test_remove_extraneous_vep_annotations(): + """ + Test remove_extraneous_vep_annotations() + """ + annotation = [{'Consequence': 'frameshift_variant'}, + {'Consequence': 'feature_elongation&TF_binding_site_variant'}] + assert utils.remove_extraneous_vep_annotations(annotation) == [{'Consequence': 'frameshift_variant'}] + + +def test_worst_csq_from_csq(): + """ + Test worst_csq_from_csq() + """ + variant = lookups.get_variant('SweGen', 16269941, '22', 'G', 'C') + res = utils.worst_csq_from_csq(variant['vep_annotations'][0]['Consequence']) + assert res == 'splice_region_variant' + res = utils.worst_csq_from_csq('non_coding_exon_variant&nc_transcript_variant') + assert res == 'non_coding_exon_variant' + + +def test_worst_csq_from_list(): + """ + Test worst_csq_from_list() + """ + csqs = ['frameshift_variant', 'missense_variant'] + assert utils.worst_csq_from_list(csqs) == 'frameshift_variant' + + +def test_worst_csq_index(): + """ + Test worst_csq_index() + """ + csqs = ['frameshift_variant', 'missense_variant'] + assert utils.worst_csq_index(csqs) == 4 + + +def test_worst_csq_with_vep(): + """ + Test worst_csq_from_vep() + """ + veps = [{'SYMBOL': '1', 'Consequence': 'intergenic_variant', 'CANONICAL': ''}, + {'SYMBOL': '2', 'Consequence': 'frameshift_variant', 'CANONICAL': ''}, + {'SYMBOL': '3', 'Consequence': 'intron_variant', 'CANONICAL': ''}, + {'SYMBOL': '4', 'Consequence': 'stop_lost', 'CANONICAL': ''}] + res = utils.worst_csq_with_vep(veps) + assert res == {'SYMBOL': '2', 'Consequence': 'frameshift_variant', + 'CANONICAL': '', 'major_consequence': 'frameshift_variant'} + + veps = [{'SYMBOL': '1', 'Consequence': 'frameshift_variant', 'CANONICAL': 'YES'}, + {'SYMBOL': '2', 'Consequence': 'frameshift_variant', 'CANONICAL': ''}, + {'SYMBOL': '3', 'Consequence': 'intron_variant', 'CANONICAL': ''}, + {'SYMBOL': '4', 'Consequence': 'stop_lost', 'CANONICAL': ''}] + res = utils.worst_csq_with_vep(veps) + assert res == {'SYMBOL': '1', 'Consequence': 'frameshift_variant', + 'CANONICAL': 'YES', 'major_consequence': 'frameshift_variant'} + assert not utils.worst_csq_with_vep([]) diff --git a/backend/modules/browser/utils.py b/backend/modules/browser/utils.py index 68350916c..67034bfe2 100644 --- a/backend/modules/browser/utils.py +++ b/backend/modules/browser/utils.py @@ -1,7 +1,60 @@ import logging -from operator import itemgetter +from . import lookups + +# for coverage AF_BUCKETS = [0.0001, 0.0002, 0.0005, 0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1] +EXON_PADDING = 50 + +CHROMOSOMES = ['chr%s' % x for x in range(1, 23)] +CHROMOSOMES.extend(['chrX', 'chrY', 'chrM']) +CHROMOSOME_TO_CODE = { item: i+1 for i, item in enumerate(CHROMOSOMES) } + +# Note that this is the current as of v81 with some included for backwards compatibility (VEP <= 75) + +CSQ_ORDER = ["transcript_ablation", +"splice_acceptor_variant", +"splice_donor_variant", +"stop_gained", +"frameshift_variant", +"stop_lost", +"start_lost", # new in v81 +"initiator_codon_variant", # deprecated +"transcript_amplification", +"inframe_insertion", +"inframe_deletion", +"missense_variant", +"protein_altering_variant", # new in v79 +"splice_region_variant", +"incomplete_terminal_codon_variant", +"stop_retained_variant", +"synonymous_variant", +"coding_sequence_variant", +"mature_miRNA_variant", +"5_prime_UTR_variant", +"3_prime_UTR_variant", +"non_coding_transcript_exon_variant", +"non_coding_exon_variant", # deprecated +"intron_variant", +"NMD_transcript_variant", +"non_coding_transcript_variant", +"nc_transcript_variant", # deprecated +"upstream_gene_variant", +"downstream_gene_variant", +"TFBS_ablation", +"TFBS_amplification", +"TF_binding_site_variant", +"regulatory_region_ablation", +"regulatory_region_amplification", +"feature_elongation", +"regulatory_region_variant", +"feature_truncation", +"intergenic_variant", +""] + +CSQ_ORDER_DICT = {csq:i for i,csq in enumerate(CSQ_ORDER)} +REV_CSQ_ORDER_DICT = dict(enumerate(CSQ_ORDER)) + METRICS = [ 'BaseQRankSum', 'ClippingRankSum', @@ -15,61 +68,38 @@ 'VQSLOD' ] +PROTEIN_LETTERS_1TO3 = { + 'A': 'Ala', 'C': 'Cys', 'D': 'Asp', 'E': 'Glu', + 'F': 'Phe', 'G': 'Gly', 'H': 'His', 'I': 'Ile', + 'K': 'Lys', 'L': 'Leu', 'M': 'Met', 'N': 'Asn', + 'P': 'Pro', 'Q': 'Gln', 'R': 'Arg', 'S': 'Ser', + 'T': 'Thr', 'V': 'Val', 'W': 'Trp', 'Y': 'Tyr', + 'X': 'Ter', '*': 'Ter', 'U': 'Sec' +} -def add_transcript_coordinate_to_variants(sdb, variant_list, transcript_id): - """ - Each variant has a 'xpos' and 'pos' positional attributes. - This method takes a list of variants and adds a third position: the "transcript coordinates". - This is defined as the distance from the start of the transcript, in coding bases. - So a variant in the 7th base of the 6th exon of a transcript will have a transcript coordinate of - the sum of the size of the first 5 exons) + 7 - This is 0-based, so a variant in the first base of the first exon has a transcript coordinate of 0. - - You may want to add transcript coordinates for multiple transcripts, so this is stored in a variant as - variant['transcript_coordinates'][transcript_id] - - If a variant in variant_list does not have a `transcript_coordinates` dictionary, we create one - - If a variant start position for some reason does not fall in any exons in this transcript, its coordinate is 0. - This is perhaps logically inconsistent, - but it allows you to spot errors quickly if there's a pileup at the first base. - `None` would just break things. - - Consider the behavior if a 20 base deletion deletes parts of two exons. - I think the behavior in this method is consistent, but beware that it might break things downstream. - Edits variant_list in place; no return val +def add_consequence_to_variants(variant_list:list): """ + Add information about variant consequence to multiple variants - import lookups - # make sure exons is sorted by (start, end) - exons = sorted(lookups.get_exons_in_transcript(sdb, transcript_id), key=itemgetter('start', 'stop')) - - # offset from start of base for exon in ith position (so first item in this list is always 0) - exon_offsets = [0 for i in range(len(exons))] - for i, exon in enumerate(exons): - for j in range(i+1, len(exons)): - exon_offsets[j] += exon['stop'] - exon['start'] - - for variant in variant_list: - if 'transcript_coordinates' not in variant: - variant['transcript_coordinates'] = {} - variant['transcript_coordinates'][transcript_id] = 0 - for i, exon in enumerate(exons): - if exon['start'] <= variant['pos'] <= exon['stop']: - variant['transcript_coordinates'][transcript_id] = exon_offsets[i] + variant['pos'] - exon['start'] - - -def xpos_to_pos(xpos): - return int(xpos % 1e9) - - -def add_consequence_to_variants(variant_list): + Args: + variant_list (list): list of variants + datatype (str): type of data + item (str): query item + """ for variant in variant_list: add_consequence_to_variant(variant) -def add_consequence_to_variant(variant): +def add_consequence_to_variant(variant:dict): + """ + Add information about variant consequence to a variant + + Args: + variant (dict): variant information + """ + if not variant: + return worst_csq = worst_csq_with_vep(variant['vep_annotations']) variant['major_consequence'] = '' if worst_csq is None: @@ -81,23 +111,128 @@ def add_consequence_to_variant(variant): variant['HGVS'] = get_proper_hgvs(worst_csq) variant['CANONICAL'] = worst_csq['CANONICAL'] - if csq_order_dict[variant['major_consequence']] <= csq_order_dict["frameshift_variant"]: + if CSQ_ORDER_DICT[variant['major_consequence']] <= CSQ_ORDER_DICT["frameshift_variant"]: variant['category'] = 'lof_variant' for annotation in variant['vep_annotations']: if annotation['LoF'] == '': annotation['LoF'] = 'NC' annotation['LoF_filter'] = 'Non-protein-coding gene' - elif csq_order_dict[variant['major_consequence']] <= csq_order_dict["missense_variant"]: + elif CSQ_ORDER_DICT[variant['major_consequence']] <= CSQ_ORDER_DICT["missense_variant"]: # Should be noted that this grabs inframe deletion, etc. variant['category'] = 'missense_variant' - elif csq_order_dict[variant['major_consequence']] <= csq_order_dict["synonymous_variant"]: + elif CSQ_ORDER_DICT[variant['major_consequence']] <= CSQ_ORDER_DICT["synonymous_variant"]: variant['category'] = 'synonymous_variant' else: variant['category'] = 'other_variant' variant['flags'] = get_flags_from_variant(variant) + return + + +def annotation_severity(annotation:dict): + """ + Evaluate severity of the consequences; "bigger is more important". + + Args: + annotation (dict): vep_annotation from a variant + + Returns: + float: severity score + """ + rv = -CSQ_ORDER_DICT[worst_csq_from_csq(annotation['Consequence'])] + if annotation['CANONICAL'] == 'YES': + rv += 0.1 + return rv + + +def get_coverage(dataset:str, datatype:str, item:str, ds_version:str=None): + """ + Retrieve coverage for a gene/region/transcript + Args: + dataset (str): short name of the dataset + datatype (str): type of "region" (gene/region/transcript) + item (str): the datatype item to look up + ds_version (str): the dataset version + + Returns: + dict: start, stop, coverage list + """ + ret = {'coverage':[]} + + if datatype == 'gene': + gene = lookups.get_gene(dataset, item) + if gene: + transcript = lookups.get_transcript(dataset, gene['canonical_transcript']) + if transcript: + start = transcript['start'] - EXON_PADDING + stop = transcript['stop'] + EXON_PADDING + ret['coverage'] = lookups.get_coverage_for_transcript(dataset, transcript['chrom'], start, stop, ds_version) + elif datatype == 'region': + try: + chrom, start, stop = item.split('-') + start = int(start) + stop = int(stop) + except ValueError: + return {'coverage': [], 'bad_region':True} + if is_region_too_large(start, stop): + return {'coverage': [], 'region_too_large': True} + ret['coverage'] = lookups.get_coverage_for_bases(dataset, chrom, start, stop, ds_version) + elif datatype == 'transcript': + transcript = lookups.get_transcript(dataset, item) + if transcript: + start = transcript['start'] - EXON_PADDING + stop = transcript['stop'] + EXON_PADDING + ret['coverage'] = lookups.get_coverage_for_transcript(dataset, transcript['chrom'], start, stop, ds_version) + return ret + + +def get_coverage_pos(dataset:str, datatype:str, item:str, ds_version:str=None): + """ + Retrieve coverage range + + Args: + dataset (str): short name of the dataset + datatype (str): type of "region" (gene/region/transcript) + item (str): the datatype item to look up -def get_flags_from_variant(variant): + Returns: + dict: start, stop, chromosome + """ + ret = {'start':None, 'stop':None, 'chrom':None} + + if datatype == 'region': + chrom, start, stop = item.split('-') + if start and stop and chrom: + ret['start'] = int(start) + ret['stop'] = int(stop) + ret['chrom'] = chrom + else: + if datatype == 'gene': + gene = lookups.get_gene(dataset, item) + transcript = lookups.get_transcript(dataset, gene['canonical_transcript'], ds_version) + elif datatype == 'transcript': + transcript = lookups.get_transcript(dataset, item, ds_version) + if transcript: + ret['start'] = transcript['start'] - EXON_PADDING + ret['stop'] = transcript['stop'] + EXON_PADDING + ret['chrom'] = transcript['chrom'] + + return ret + + +def get_flags_from_variant(variant:dict): + """ + Get flags from variant. + Checks for: + - MNP (identical length of reference and variant) + - LoF (loss of function) + + Args: + variant (dict): a variant + + Returns: + list: flags for the variant + """ flags = [] if 'mnps' in variant: flags.append('MNP') @@ -111,197 +246,266 @@ def get_flags_from_variant(variant): return flags -protein_letters_1to3 = { - 'A': 'Ala', 'C': 'Cys', 'D': 'Asp', 'E': 'Glu', - 'F': 'Phe', 'G': 'Gly', 'H': 'His', 'I': 'Ile', - 'K': 'Lys', 'L': 'Leu', 'M': 'Met', 'N': 'Asn', - 'P': 'Pro', 'Q': 'Gln', 'R': 'Arg', 'S': 'Ser', - 'T': 'Thr', 'V': 'Val', 'W': 'Trp', 'Y': 'Tyr', - 'X': 'Ter', '*': 'Ter', 'U': 'Sec' -} +def get_proper_hgvs(annotation:dict): + """ + Get HGVS for change, either at transcript or protein level. + Args: + annotation (dict): VEP annotation with HGVS information -def get_proper_hgvs(csq): + Returns: + str: variant effect at aa level in HGVS format (p.), None if parsing fails + """ # Needs major_consequence - if csq['major_consequence'] in ('splice_donor_variant', 'splice_acceptor_variant', 'splice_region_variant'): - return get_transcript_hgvs(csq) - - return get_protein_hgvs(csq) - - -def get_transcript_hgvs(csq): - return csq['HGVSc'].split(':')[-1] + try: + if annotation['major_consequence'] in ('splice_donor_variant', + 'splice_acceptor_variant', + 'splice_region_variant'): + return get_transcript_hgvs(annotation) + return get_protein_hgvs(annotation) + except KeyError: + return None def get_protein_hgvs(annotation): """ - Takes consequence dictionary, returns proper variant formatting for synonymous variants + Aa changes in HGVS format. + + Args: + annotation (dict): VEP annotation with HGVS information + + Returns: + str: variant effect at aa level in HGVS format (p.), None if parsing fails """ - if '%3D' in annotation['HGVSp']: # "%3D" is "=" - try: - amino_acids = ''.join([protein_letters_1to3[x] for x in annotation['Amino_acids']]) + try: + if '%3D' in annotation['HGVSp']: # "%3D" is "=" + amino_acids = ''.join([PROTEIN_LETTERS_1TO3[aa] for aa in annotation['Amino_acids']]) return "p." + amino_acids + annotation['Protein_position'] + amino_acids - except KeyError: - logging.error("Could not fetch protein hgvs - unknown amino acid") - return annotation['HGVSp'].split(':')[-1] + return annotation['HGVSp'].split(':')[-1] + except KeyError: + logging.error("Could not fetch protein hgvs") + return None -# Note that this is the current as of v81 with some included for backwards compatibility (VEP <= 75) -csq_order = ["transcript_ablation", -"splice_acceptor_variant", -"splice_donor_variant", -"stop_gained", -"frameshift_variant", -"stop_lost", -"start_lost", # new in v81 -"initiator_codon_variant", # deprecated -"transcript_amplification", -"inframe_insertion", -"inframe_deletion", -"missense_variant", -"protein_altering_variant", # new in v79 -"splice_region_variant", -"incomplete_terminal_codon_variant", -"stop_retained_variant", -"synonymous_variant", -"coding_sequence_variant", -"mature_miRNA_variant", -"5_prime_UTR_variant", -"3_prime_UTR_variant", -"non_coding_transcript_exon_variant", -"non_coding_exon_variant", # deprecated -"intron_variant", -"NMD_transcript_variant", -"non_coding_transcript_variant", -"nc_transcript_variant", # deprecated -"upstream_gene_variant", -"downstream_gene_variant", -"TFBS_ablation", -"TFBS_amplification", -"TF_binding_site_variant", -"regulatory_region_ablation", -"regulatory_region_amplification", -"feature_elongation", -"regulatory_region_variant", -"feature_truncation", -"intergenic_variant", -""] -assert len(csq_order) == len(set(csq_order)) # No dupes! -csq_order_dict = {csq:i for i,csq in enumerate(csq_order)} -rev_csq_order_dict = dict(enumerate(csq_order)) -assert all(csq == rev_csq_order_dict[csq_order_dict[csq]] for csq in csq_order) +def get_transcript_hgvs(annotation:dict): + """ + Nucleotide change in HGVS format. + Args: + annotation (dict): VEP annotation with HGVS information -def remove_extraneous_vep_annotations(annotation_list): - return [ann for ann in annotation_list if worst_csq_index(ann['Consequence'].split('&')) <= csq_order_dict['intron_variant']] + Returns: + str: variant effect at nucleotide level in HGVS format (c.), None if parsing fails + """ + try: + return annotation['HGVSc'].split(':')[-1] + except KeyError: + return None -def worst_csq_index(csq_list): - """ - Input list of consequences (e.g. ['frameshift_variant', 'missense_variant']) - Return index of the worst consequence (In this case, index of 'frameshift_variant', so 4) - Works well with worst_csq_index('non_coding_exon_variant&nc_transcript_variant'.split('&')) +def get_variant_list(dataset:str, datatype:str, item:str, ds_version:str=None): """ - return min([csq_order_dict[csq] for csq in csq_list]) + Retrieve variants for a datatype + Args: + dataset (str): dataset short name + datatype (str): type of data + item (str): query item + ds_version (str): dataset version -def worst_csq_from_list(csq_list): + Returns: + dict: {variants:list, headers:list} """ - Input list of consequences (e.g. ['frameshift_variant', 'missense_variant']) - Return the worst consequence (In this case, 'frameshift_variant') - Works well with worst_csq_from_list('non_coding_exon_variant&nc_transcript_variant'.split('&')) + headers = [['variant_id','Variant'], ['chrom','Chrom'], ['pos','Position'], + ['HGVS','Consequence'], ['filter','Filter'], ['major_consequence','Annotation'], + ['flags','Flags'], ['allele_count','Allele Count'], ['allele_num','Allele Number'], + ['hom_count','Number of Homozygous Alleles'], ['allele_freq','Allele Frequency']] + + if datatype == 'gene': + variants = lookups.get_variants_in_gene(dataset, item, ds_version) + elif datatype == 'region': + try: + chrom, start, stop = item.split('-') + start = int(start) + stop = int(stop) + except ValueError: + return None + + if is_region_too_large(start, stop): + return {'variants': [], 'headers': [], 'region_too_large': True} + variants = lookups.get_variants_in_region(dataset, chrom, start, stop, ds_version) + elif datatype == 'transcript': + variants = lookups.get_variants_in_transcript(dataset, item, ds_version) + + if datatype == 'transcript': + transcript = lookups.get_transcript(dataset, item, ds_version) + if not transcript: + return None + refgene = transcript['gene_id'] + + for variant in variants: + if datatype in ('gene', 'transcript'): + anno = None + if datatype == 'transcript': + anno = [ann for ann in variant['vep_annotations'] if ann['Feature'] == item] + if not anno: + anno = [ann for ann in variant['vep_annotations'] if ann['Gene'] == refgene] + else: + anno = [ann for ann in variant['vep_annotations'] if ann['Gene'] == item] + if anno: + variant['vep_annotations'] = anno + + add_consequence_to_variants(variants) + + for variant in variants: + remove_extraneous_information(variant) + + # Format output + def format_variant(variant): + variant['major_consequence'] = (variant['major_consequence'].replace('_variant','') + .replace('_prime_', '\'') + .replace('_', ' ')) + + # This is so an array values turns into a comma separated string instead + return {k: ", ".join(v) if isinstance(v,list) else v for k, v in variant.items()} + + variants = list(map(format_variant, variants)) + + return {'variants': variants, 'headers': headers} + + +def order_vep_by_csq(annotation_list:list): """ - return rev_csq_order_dict[worst_csq_index(csq_list)] + Adds "major_consequence" to each annotation, orders by severity. + Args: + annotation_list (list): VEP annotations (as dict) -def worst_csq_from_csq(csq): - """ - Input possibly &-filled csq string (e.g. 'non_coding_exon_variant&nc_transcript_variant') - Return the worst consequence (In this case, 'non_coding_exon_variant') + Returns: + list: annotations ordered by major consequence severity """ - return rev_csq_order_dict[worst_csq_index(csq.split('&'))] + for ann in annotation_list: + try: + ann['major_consequence'] = worst_csq_from_csq(ann['Consequence']) + except KeyError: + ann['major_consequence'] = '' + return sorted(annotation_list, key=(lambda ann:CSQ_ORDER_DICT[ann['major_consequence']])) + +def is_region_too_large(start:int, stop:int): + ''' + Evaluates whether the size of a region is larger than maximum query + Args: + start (int): Start position of the region + stop (int): End position of the region -def order_vep_by_csq(annotation_list): + Returns: + bool: True if too large + ''' + region_limit = 100000 + return int(stop)-int(start) > region_limit + + +def parse_dataset(dataset, ds_version=None): """ - Adds "major_consequence" to each annotation. - Returns them ordered from most deleterious to least. + Check/parse if the dataset name is in the beacon form: + ``reference:dataset:version`` + + Args: + dataset (str): short name of the dataset + ds_version (str): the dataset version + + Returns: + tuple: (dataset, version) """ - for ann in annotation_list: - ann['major_consequence'] = worst_csq_from_csq(ann['Consequence']) - return sorted(annotation_list, key=(lambda ann:csq_order_dict[ann['major_consequence']])) + beacon_style = dataset.split(':') + if len(beacon_style) == 3: + return (beacon_style[1], beacon_style[2]) + else: + return (dataset, ds_version) + + +def remove_extraneous_information(variant:dict): + ''' + Remove information that is not used in the frontend from a variant + + Args: + variant (dict): variant data from database + ''' + del variant['id'] + del variant['dataset_version'] + del variant['orig_alt_alleles'] + del variant['site_quality'] + del variant['vep_annotations'] -def worst_csq_with_vep(annotation_list): +def remove_extraneous_vep_annotations(annotation_list:list): """ - Takes list of VEP annotations [{'Consequence': 'frameshift', Feature: 'ENST'}, ...] - Returns most severe annotation (as full VEP annotation [{'Consequence': 'frameshift', Feature: 'ENST'}]) - Also tacks on "major_consequence" for that annotation (i.e. worst_csq_from_csq) + Remove annotations with low-impact consequences (less than intron variant) + + Args: + annotation_list (list): VEP annotations (as dict) + + Returns: + list: VEP annotations with higher impact """ - if not annotation_list: - return None - worst = max(annotation_list, key=annotation_severity) - worst['major_consequence'] = worst_csq_from_csq(worst['Consequence']) - return worst + return [ann for ann in annotation_list + if worst_csq_index(ann['Consequence'].split('&')) <= CSQ_ORDER_DICT['intron_variant']] -def annotation_severity(annotation): - "Bigger is more important." - rv = -csq_order_dict[worst_csq_from_csq(annotation['Consequence'])] - if annotation['CANONICAL'] == 'YES': - rv += 0.1 - return rv +def worst_csq_from_list(csq_list:list): + """ + Choose the worst consequence -CHROMOSOMES = ['chr%s' % x for x in range(1, 23)] -CHROMOSOMES.extend(['chrX', 'chrY', 'chrM']) -CHROMOSOME_TO_CODE = { item: i+1 for i, item in enumerate(CHROMOSOMES) } + Args: + csq_list (list): list of consequences + + Returns: + str: the worst consequence + """ + return REV_CSQ_ORDER_DICT[worst_csq_index(csq_list)] -def get_single_location(chrom, pos): +def worst_csq_from_csq(csq:str): """ - Gets a single location from chromosome and position - chr must be actual chromosme code (chrY) and pos must be integer + Find worst consequence in a possibly &-filled consequence string - Borrowed from xbrowse + Args: + csq (str): string of consequences, seperated with & (if multiple) + + Returns: + str: the worst consequence """ - return CHROMOSOME_TO_CODE[chrom] * int(1e9) + pos + return REV_CSQ_ORDER_DICT[worst_csq_index(csq.split('&'))] -def get_xpos(chrom, pos): +def worst_csq_index(csq_list:list): """ - Borrowed from xbrowse + Find the index of the worst consequence. + Corresponds to the lowest value (index) from CSQ_ORDER_DICT + + Args: + csq_list (list): consequences + + Returns: + int: index in CSQ_ODER_DICT of the worst consequence """ - if not chrom.startswith('chr'): - chrom = 'chr{}'.format(chrom) - return get_single_location(chrom, int(pos)) + return min([CSQ_ORDER_DICT[csq] for csq in csq_list]) -def get_minimal_representation(pos, ref, alt): +def worst_csq_with_vep(annotation_list:list): """ - Get the minimal representation of a variant, based on the ref + alt alleles in a VCF - This is used to make sure that multiallelic variants in different datasets, - with different combinations of alternate alleles, can always be matched directly. + Choose the vep annotation with the most severe consequence + Adds a"major_consequence" field for that annotation - Note that chromosome is ignored here - in xbrowse, we'll probably be dealing with 1D coordinates Args: - pos (int): genomic position in a chromosome (1-based) - ref (str): ref allele string - alt (str): alt allele string + annotation_list (list): VEP annotations + Returns: - tuple: (pos, ref, alt) of remapped coordinate - """ - pos = int(pos) - # If it's a simple SNV, don't remap anything - if len(ref) == 1 and len(alt) == 1: - return pos, ref, alt - - # strip off identical suffixes - while(alt[-1] == ref[-1] and min(len(alt),len(ref)) > 1): - alt = alt[:-1] - ref = ref[:-1] - # strip off identical prefixes and increment position - while(alt[0] == ref[0] and min(len(alt),len(ref)) > 1): - alt = alt[1:] - ref = ref[1:] - pos += 1 - return pos, ref, alt + dict: the annotation with the most severe consequence + """ + if not annotation_list: + return None + worst = max(annotation_list, key=annotation_severity) + worst['major_consequence'] = worst_csq_from_csq(worst['Consequence']) + return worst diff --git a/backend/requirements.txt b/backend/requirements.txt index 2b1534135..84c8e8d82 100644 --- a/backend/requirements.txt +++ b/backend/requirements.txt @@ -6,7 +6,6 @@ chardet==3.0.4 idna==2.6 packaging==16.8 peewee==2.9.2 -pymongo==3.4.0 pyparsing==2.2.0 requests==2.18.4 six==1.10.0 diff --git a/backend/settings.py b/backend/settings.py index 249cd91a9..ff925bb3a 100644 --- a/backend/settings.py +++ b/backend/settings.py @@ -32,13 +32,6 @@ ## Generated with base64.b64encode(uuid.uuid4().bytes + uuid.uuid4().bytes) cookie_secret = json_settings["cookieSecret"] -# Mongodb settings -mongo_host = json_settings["mongoHost"] -mongo_port = json_settings["mongoPort"] -mongo_user = json_settings["mongoUser"] -mongo_password = json_settings["mongoPassword"] -mongo_databases = json_settings["mongoDatabases"] - # PostgreSQL settings psql_host = json_settings["postgresHost"] psql_port = json_settings["postgresPort"] diff --git a/backend/test_requirements.txt b/backend/test_requirements.txt new file mode 100644 index 000000000..c75c448bb --- /dev/null +++ b/backend/test_requirements.txt @@ -0,0 +1 @@ +pytest-cov diff --git a/frontend/src/js/controller.browserController.js b/frontend/src/js/controller.browserController.js index 6537e6c4c..17e700ef9 100644 --- a/frontend/src/js/controller.browserController.js +++ b/frontend/src/js/controller.browserController.js @@ -6,7 +6,7 @@ localThis.query = ""; localThis.suggestions = ""; localThis.activeSuggestion = -1; - localThis.orderByField = "variantId"; + localThis.orderByField = "pos"; localThis.reverseSort = false; localThis.coverage = {}; @@ -54,62 +54,96 @@ if ($routeParams.transcript) { localThis.itemType = "transcript"; localThis.item = $routeParams.transcript; - Browser.getTranscript($routeParams.dataset, $routeParams.transcript).then( function(data) { - localThis.transcript = data.transcript; - localThis.gene = data.gene; - localThis.coverage.region.exons = data.exons; - }); + Browser.getTranscript($routeParams.dataset, $routeParams.version, $routeParams.transcript) + .then( function(data) { + localThis.transcript = data.transcript; + localThis.gene = data.gene; + localThis.coverage.region.exons = data.exons; + }) + .catch((err) => { + localThis.transcript = {"statusCode": err.status, + "statusText": err.statusText}; + }); +; } if ($routeParams.region) { localThis.itemType = "region"; localThis.item = $routeParams.region; - Browser.getRegion($routeParams.dataset, $routeParams.region).then( function(data) { - localThis.region = data.region; - }); + Browser.getRegion($routeParams.dataset, $routeParams.version, $routeParams.region) + .then( function(data) { + localThis.region = data.region; + }) + .catch((err) => { + localThis.region = {"statusCode": err.status, + "statusText": err.statusText, + "variantId": $routeParams.region}; + }); } if ($routeParams.gene) { localThis.itemType = "gene"; localThis.item = $routeParams.gene; - Browser.getGene($routeParams.dataset, $routeParams.gene).then( function(data) { - localThis.gene = data.gene; - localThis.transcripts = data.transcripts; - localThis.coverage.region.exons = data.exons; - }); + Browser.getGene($routeParams.dataset, $routeParams.version, $routeParams.gene) + .then( function(data) { + localThis.gene = data.gene; + localThis.transcripts = data.transcripts; + localThis.coverage.region.exons = data.exons; + }) + .catch((err) => { + localThis.gene = {"statusCode": err.status, + "statusText": err.statusText}; + }); } - if (localThis.itemType) { - Browser.getVariants($routeParams.dataset, localThis.itemType, localThis.item).then( function(data) { - localThis.variants = data.variants; - localThis.headers = data.headers; - - // TODO Move to function later - let mapFunction = function(variant) { - variant.isPass = variant.filter == "PASS"; - variant.isLof = variant.flags == "LC LoF"; - variant.isMissense = variant.majorConsequence == "missense"; - }; - localThis.variants.map(mapFunction); - - localThis.filterVariants(); - - }); - Browser.getCoveragePos($routeParams.dataset, localThis.itemType, localThis.item).then( function(data) { - localThis.coverage.region.start = data.start; - localThis.coverage.region.stop = data.stop; - localThis.coverage.region.chrom = data.chrom; - }); - Browser.getCoverage($routeParams.dataset, localThis.itemType, localThis.item).then(function(data) { - localThis.coverage.data = data.coverage; - localThis.coverage.loaded = true; - }, function() { - localThis.coverage.loaded = true; - }); + if (localThis.itemType) { + Browser.getVariants($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item) + .then( function(data) { + localThis.variants = data.variants; + localThis.headers = data.headers; + + // TODO Move to function later + let mapFunction = function(variant) { + variant.isPass = variant.filter == "PASS"; + variant.isLof = variant.flags == "LC LoF"; + variant.isMissense = variant.majorConsequence == "missense"; + }; + localThis.variants.map(mapFunction); + + localThis.filterVariants(); + localThis.variants.loaded = true; + }) + .catch((err) => { + localThis.variants = {"statusCode": err.status, + "statusText": err.statusText, + "loaded": true,}; + }); + Browser.getCoveragePos($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item) + .then( function(data) { + localThis.coverage.region.start = data.start; + localThis.coverage.region.stop = data.stop; + localThis.coverage.region.chrom = data.chrom; + }); + Browser.getCoverage($routeParams.dataset, $routeParams.version, localThis.itemType, localThis.item) + .then(function(data) { + localThis.coverage.data = data.coverage; + localThis.coverage.loaded = true; + }) + .catch((err) => { + localThis.coverage = {"statusCode": err.status, + "statusText": err.statusText, + "loaded": true,}; + }); } if ($routeParams.variant) { - Browser.getVariant($routeParams.dataset, $routeParams.variant).then( function(data) { - localThis.variant = data.variant; - }); + Browser.getVariant($routeParams.dataset, $routeParams.version, $routeParams.variant) + .then( function(data) { + localThis.variant = data.variant; + }) + .catch((err) => { + localThis.variant = {"statusCode": err.status, + "statusText": err.statusText}; + }); + } - Dataset.getDataset($routeParams.dataset, $routeParams.version) + Dataset.getDataset($routeParams.dataset, $routeParams.version, $routeParams.version) .then(function(data) { localThis.dataset = data.dataset; }, @@ -131,7 +165,7 @@ localThis.query = query; } if (localThis.query) { - Browser.search($routeParams.dataset, localThis.query).then( function(data) { + Browser.search($routeParams.dataset, $routeParams.version, localThis.query).then( function(data) { var url = browserLink(`${data.type}/${data.value}`); if ( data.type == "error" || data.type == "not_found" ) { @@ -145,7 +179,7 @@ function autocomplete() { localThis.activeSuggestion = -1; if (localThis.query) { - Browser.autocomplete($routeParams.dataset, localThis.query) + Browser.autocomplete($routeParams.dataset, $routeParams.version, localThis.query) .then( function(data) { localThis.suggestions = data.values; }); diff --git a/frontend/src/js/factory.browser.js b/frontend/src/js/factory.browser.js index 66959bcd0..4cb4ae1cc 100644 --- a/frontend/src/js/factory.browser.js +++ b/frontend/src/js/factory.browser.js @@ -13,56 +13,65 @@ getCoveragePos:getCoveragePos, }; - function getGene(dataset, gene) { - return $http.get("/api/datasets/" + dataset + "/browser/gene/" + gene).then(function(data) { + function baseUrl(dataset, version) { + var url = "/api/datasets/" + dataset + "/"; + if ( version ) { + url += "version/" + version + "/" + } + url += 'browser/'; + return url; + } + + function getGene(dataset, version, gene) { + return $http.get(baseUrl(dataset, version) + "gene/" + gene).then(function(data) { return data.data; }); } - function getRegion(dataset, region) { - return $http.get("/api/datasets/" + dataset + "/browser/region/" + region).then(function(data) { + function getRegion(dataset, version, region) { + return $http.get(baseUrl(dataset, version) + "region/" + region).then(function(data) { return data.data; }); } - function getTranscript(dataset, transcript) { - return $http.get("/api/datasets/" + dataset + "/browser/transcript/" + transcript).then(function(data) { + function getTranscript(dataset, version, transcript) { + return $http.get(baseUrl(dataset, version) + "transcript/" + transcript).then(function(data) { return data.data; }); } - function getVariant(dataset, variant) { - return $http.get("/api/datasets/" + dataset + "/browser/variant/" + variant).then(function(data) { + function getVariant(dataset, version, variant) { + return $http.get(baseUrl(dataset, version) + "variant/" + variant).then(function(data) { return data.data; - }); + }); } - function search(dataset, query) { - return $http.get("/api/datasets/" + dataset + "/browser/search/" + query).then(function(data) { + function search(dataset, version, query) { + return $http.get(baseUrl(dataset, version) + "search/" + query).then(function(data) { return data.data; }); } - function autocomplete(dataset, query) { - return $http.get("/api/datasets/" + dataset + "/browser/autocomplete/" + query).then(function(data) { + function autocomplete(dataset, version, query) { + return $http.get(baseUrl(dataset, version) + "autocomplete/" + query).then(function(data) { return data.data; }); } - function getVariants(dataset, datatype, item) { - return $http.get("api/datasets/" + dataset + "/browser/variants/" + datatype + "/" + item).then(function(data) { + function getVariants(dataset, version, datatype, item) { + return $http.get(baseUrl(dataset, version) + "variants/" + datatype + "/" + item).then(function(data) { return data.data; }); } - function getCoverage(dataset, datatype, item) { - return $http.get("api/datasets/" + dataset + "/browser/coverage/" + datatype + "/" + item).then(function(data) { + function getCoverage(dataset, version, datatype, item) { + return $http.get(baseUrl(dataset, version) + "coverage/" + datatype + "/" + item).then(function(data) { return data.data; }); } - function getCoveragePos(dataset, datatype, item) { - return $http.get("api/datasets/" + dataset + "/browser/coverage_pos/" + datatype + "/" + item).then(function(data) { + function getCoveragePos(dataset, version, datatype, item) { + return $http.get(baseUrl(dataset, version) + "coverage_pos/" + datatype + "/" + item).then(function(data) { return data.data; }); } diff --git a/frontend/templates/ng-templates/browser-coverage-plot.jj2 b/frontend/templates/ng-templates/browser-coverage-plot.jj2 index ea004d857..1468824e2 100644 --- a/frontend/templates/ng-templates/browser-coverage-plot.jj2 +++ b/frontend/templates/ng-templates/browser-coverage-plot.jj2 @@ -1,57 +1,64 @@ -

Gene summary

-

(Coverage shown for canonical transcript: {{ ctrl.gene.canonicalTranscript }})

-

Mean coverage: {{ ctrl.dataset.avgSeqDepth }} (entire dataset)

-
+
+

Unable to load the coverage information.

+

Reason: {{ ctrl.coverage.statusCode }} {{ ctrl.coverage.statusText }}

+
+ +
+

Gene summary

+

(Coverage shown for canonical transcript: {{ ctrl.gene.canonicalTranscript }})

+

Mean coverage: {{ ctrl.dataset.avgSeqDepth }} (entire dataset)

+
- - - - - - - - - + + + + + + + + + - +
- - - - - - + + + + + +
-
+
-
+
- -
-
-
+ +
+
+
+
diff --git a/frontend/templates/ng-templates/browser-gene.html b/frontend/templates/ng-templates/browser-gene.html index 15439acc4..a6ab6b16d 100644 --- a/frontend/templates/ng-templates/browser-gene.html +++ b/frontend/templates/ng-templates/browser-gene.html @@ -2,7 +2,12 @@ [% extends "ng-templates/dataset-base.jj2" %] [% block controller %]browserController[% endblock %] [% block contents %] -
+
+

Unable to load the gene information.

+

Reason: {{ ctrl.gene.statusCode }} {{ ctrl.gene.statusText }}

+
+ +

Gene: {{ ctrl.gene.geneName }}

@@ -15,9 +20,6 @@

Gene: {{ ctrl.gene.geneName }}

{{ ctrl.gene.geneName }}
{{ ctrl.gene.fullGeneName }}
-
Number of variants
-
{{ ctrl.gene.variants.filtered }} (Including filtered: {{ ctrl.gene.variants.total }})
-
UCSC Browser
-
+
[% include "ng-templates/browser-coverage-plot.jj2" %]
@@ -136,11 +138,11 @@

Gene: {{ ctrl.gene.geneName }}

-
+
[% include "ng-templates/browser-variant-list.jj2" %]
-
+
Loading Variant List
[% endblock %] diff --git a/frontend/templates/ng-templates/browser-region.html b/frontend/templates/ng-templates/browser-region.html index f586328cd..296fbfd39 100644 --- a/frontend/templates/ng-templates/browser-region.html +++ b/frontend/templates/ng-templates/browser-region.html @@ -13,14 +13,14 @@

Region: {{ ctrl.region.chrom }}

-
-
-
-

Region too large!

-

Your region is too large. Please submit a region of at most 100 kb.

-

If you require larger regions, please see our Download page for raw data.

-
+
+
+

Region too large!

+

The region is too large. Please submit a region of at most 100 kb.

+

If you require larger regions, please see our Download page for raw data.

+
+

Invalid region!

@@ -29,6 +29,11 @@

Invalid region!

+
+

Trouble loading the region information.

+

Code: {{ ctrl.region.statusCode }} Status text: {{ ctrl.region.statusText }}

+
+
@@ -47,7 +52,7 @@

Invalid region!

-
+
[% include "ng-templates/browser-coverage-plot.jj2" %]
@@ -57,12 +62,12 @@

Invalid region!

-
+
[% include "ng-templates/browser-variant-list.jj2" %]
-
+
Loading Variant List
[% endblock %] diff --git a/frontend/templates/ng-templates/browser-transcript.html b/frontend/templates/ng-templates/browser-transcript.html index 0bb6edfcf..6645feb44 100644 --- a/frontend/templates/ng-templates/browser-transcript.html +++ b/frontend/templates/ng-templates/browser-transcript.html @@ -2,6 +2,12 @@ [% extends "ng-templates/dataset-base.jj2" %] [% block controller %]browserController[% endblock %] [% block contents %] + +
+

Unable to load the transcript information.

+

Reason: {{ ctrl.transcript.statusCode }} {{ ctrl.transcript.statusText }}

+
+

{{ ctrl.gene.name }}

{{ ctrl.gene.fullName }}

@@ -22,12 +28,12 @@

Transcript: {{ ctrl.transcript.id }} ({{ ctrl.transcript.numberOfCDS }} codi

-
+
Loading Transcript
-
+
[% include "ng-templates/browser-coverage-plot.jj2" %]
@@ -37,11 +43,11 @@

Transcript: {{ ctrl.transcript.id }} ({{ ctrl.transcript.numberOfCDS }} codi

-
+
[% include "ng-templates/browser-variant-list.jj2" %]
-
+
Loading Variant List
[% endblock %] diff --git a/frontend/templates/ng-templates/browser-variant-list.jj2 b/frontend/templates/ng-templates/browser-variant-list.jj2 index 1ee8a3d9a..7a6a0fa82 100644 --- a/frontend/templates/ng-templates/browser-variant-list.jj2 +++ b/frontend/templates/ng-templates/browser-variant-list.jj2 @@ -1,4 +1,9 @@ -
+
+

Unable to load the variants.

+

Reason: {{ ctrl.variants.statusCode }} {{ ctrl.variants.statusText }}

+
+ +
@@ -28,7 +33,11 @@ † denotes a consequence that is for a non-canonical transcript
- +
+
+ Number of variants: {{ctrl.filteredVariants.length}} (including filtered: {{ctrl.variants.length}}) +
+
diff --git a/frontend/templates/ng-templates/browser-variant.html b/frontend/templates/ng-templates/browser-variant.html index 439251727..6e318d6aa 100644 --- a/frontend/templates/ng-templates/browser-variant.html +++ b/frontend/templates/ng-templates/browser-variant.html @@ -2,7 +2,12 @@ [% extends "ng-templates/dataset-base.jj2" %] [% block controller %]browserController[% endblock %] [% block contents %] -
+ +
+

Unable to load the variant.

+

Reason: {{ ctrl.variant.statusCode }} {{ ctrl.variant.statusText }}

+
+
@@ -44,7 +49,7 @@

Warning!

{{ ctrl.variant.rsid }} -
Not found in dbSNP
+
rsID not available
Allele Frequency
{{ ctrl.variant.alleleFreq | number : 4 }}
NA (Allele Number = 0)
diff --git a/settings_sample.json b/settings_sample.json index d3310b007..50f3168ac 100644 --- a/settings_sample.json +++ b/settings_sample.json @@ -17,17 +17,6 @@ "postgresPass" : "", "postgresName" : "swefreq", - "mongoHost" : "mongodb host", - "mongoPassword" : "password", - "mongoPort" : 27017, - "mongoUser" : "exac", - "mongoDatabases": { - "Dataset": { - "db": "db-name", - "shared": "shared-db-name" - } - }, - "replyToAddress" : "no-reply@example.com", "fromAddress" : "no-reply@example.com", "mailServer" : "smtp.example.com", diff --git a/test/data/browser_test_data.sql b/test/data/browser_test_data.sql new file mode 100644 index 000000000..0284fcd5f --- /dev/null +++ b/test/data/browser_test_data.sql @@ -0,0 +1,5651 @@ +SET statement_timeout = 0; +SET lock_timeout = 0; +SET idle_in_transaction_session_timeout = 0; +SET client_encoding = 'UTF8'; +SET standard_conforming_strings = on; +SELECT pg_catalog.set_config('search_path', '', false); +SET check_function_bodies = false; +SET client_min_messages = warning; +SET row_security = off; + +COPY data.collections (id, study_name, ethnicity) FROM stdin; +1 reg undefined +\. + +COPY data.studies (id, pi_name, pi_email, contact_name, contact_email, title, study_description, publication_date, ref_doi) FROM stdin; +1 name email name email SweGen \N 2001-01-01 00:00:00 doi +\. + +COPY data.datasets (id, study, short_name, full_name, browser_uri, beacon_uri, beacon_description, avg_seq_depth, seq_type, seq_tech, seq_center, dataset_size) FROM stdin; +1 1 SweGen SweGen url \N \N 0 type method place 0 +\. + +COPY data.reference_sets (id, reference_build, reference_name, ensembl_version, gencode_version, dbnsfp_version) FROM stdin; +1 \N swegen homo_sapiens_core_75_37 19 2.9.3 +\. + +COPY data.dataset_versions (id, dataset, reference_set, dataset_version, dataset_description, terms, var_call_ref, available_from, ref_doi, data_contact_name, data_contact_link, num_variants, coverage_levels) FROM stdin; +2 1 1 20170823 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} +3 1 1 20171025 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} +1 1 1 20161223 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} +4 1 1 20180409 desc terms hg19 2001-01-01 00:00:00 doi place email \N {1,5,10,15,20,25,30,50,100} +\. + +COPY data.coverage (id, dataset_version, chrom, pos, mean, median, coverage) FROM stdin; +1 4 22 16364820 75.4499969 71 {1,1,0.999000013,0.998000026,0.998000026,0.994000018,0.976000011,0.792999983,0.170000002} +2 4 22 16364830 75.9400024 71 {1,1,0.999000013,0.999000013,0.998000026,0.994000018,0.977999985,0.801999986,0.179000005} +3 4 22 16364840 74.8899994 70 {1,1,1,0.999000013,0.996999979,0.991999984,0.976999998,0.791999996,0.166999996} +4 4 22 16364850 72.9400024 69 {1,1,0.999000013,0.999000013,0.996999979,0.991999984,0.976000011,0.772000015,0.157000005} +5 4 22 16364860 71.0599976 67 {1,1,0.999000013,0.999000013,0.996999979,0.987999976,0.973999977,0.762000024,0.143999994} +6 4 22 16364870 67.4100037 63 {1,1,0.999000013,0.998000026,0.996999979,0.986999989,0.968999982,0.722000003,0.112000003} +7 4 22 16364880 64.2600021 60 {1,1,1,0.998000026,0.994000018,0.986999989,0.958000004,0.693000019,0.0799999982} +8 4 22 16364890 60.9199982 58 {1,1,1,0.998000026,0.995000005,0.986000001,0.957000017,0.637000024,0.0560000017} +9 4 22 16364900 58.8899994 56 {1,1,1,0.998000026,0.995000005,0.98299998,0.953000009,0.611999989,0.0419999994} +10 4 22 16364910 57.5699997 54 {1,1,1,0.996999979,0.994000018,0.98299998,0.94599998,0.589999974,0.0370000005} +11 4 22 16364920 56.25 53.5 {1,1,1,0.995999992,0.990999997,0.98299998,0.938000023,0.57099998,0.0299999993} +12 4 22 16364930 55.1800003 53 {1,1,1,0.995999992,0.990999997,0.980000019,0.944000006,0.546999991,0.0250000004} +13 4 22 16364940 55.1500015 53 {1,1,1,0.996999979,0.990999997,0.976999998,0.954999983,0.555999994,0.0260000005} +14 4 22 16364950 54 52 {1,1,1,0.998000026,0.990999997,0.978999972,0.95599997,0.532000005,0.0189999994} +15 4 22 16364960 51.6800003 50 {1,1,1,0.995999992,0.99000001,0.976000011,0.940999985,0.476000011,0.0140000004} +16 4 22 16364970 50.6199989 48 {1,1,1,0.995999992,0.989000022,0.973999977,0.927999973,0.451000005,0.0109999999} +17 4 22 16364980 50.5 48.5 {1,1,1,0.996999979,0.99000001,0.975000024,0.93900001,0.451000005,0.00999999978} +18 4 22 16364990 50.8499985 49 {1,1,1,0.996999979,0.992999971,0.977999985,0.941999972,0.460000008,0.00999999978} +19 4 22 16365000 50.9799995 49 {1,1,1,0.998000026,0.991999984,0.981999993,0.941999972,0.453999996,0.00999999978} +20 4 22 16365010 51.2400017 49 {1,1,1,0.998000026,0.991999984,0.981999993,0.950999975,0.451999992,0.0109999999} +21 4 22 16365020 52.4599991 50 {1,1,1,0.998000026,0.991999984,0.981000006,0.957000017,0.488999993,0.00999999978} +22 4 22 16365030 52.9500008 51 {1,1,1,0.999000013,0.992999971,0.981999993,0.958999991,0.504999995,0.0109999999} +23 4 22 16365040 53.5299988 51 {1,1,1,0.998000026,0.995000005,0.986999989,0.959999979,0.521000028,0.0120000001} +24 4 22 16365050 54.1100006 52 {1,1,1,0.999000013,0.994000018,0.985000014,0.958000004,0.528999984,0.0160000008} +25 4 22 16365060 54.7799988 52 {1,1,1,0.998000026,0.995000005,0.985000014,0.968999982,0.555000007,0.0170000009} +26 4 22 16365070 54.7599983 52 {1,1,1,0.998000026,0.995000005,0.985000014,0.962000012,0.547999978,0.0189999994} +27 4 22 16365080 54.1599998 52 {1,1,1,0.999000013,0.992999971,0.985000014,0.957000017,0.532000005,0.0189999994} +28 4 22 16365090 53.0999985 51 {1,1,1,0.998000026,0.991999984,0.985000014,0.947000027,0.503000021,0.0189999994} +29 4 22 16365100 52.0099983 49 {1,1,1,0.996999979,0.994000018,0.981000006,0.944999993,0.469999999,0.0160000008} +30 4 22 16365110 52.3699989 50 {1,1,1,0.998000026,0.994000018,0.981000006,0.948000014,0.479000002,0.0209999997} +31 4 22 16365120 51.3300018 49 {1,1,1,0.998000026,0.995000005,0.977999985,0.93900001,0.455000013,0.0170000009} +32 4 22 16365130 50.7999992 49 {1,1,1,0.998000026,0.995000005,0.981999993,0.930999994,0.451999992,0.0149999997} +33 4 22 16365140 50.5900002 48 {1,1,1,0.999000013,0.995000005,0.976999998,0.924000025,0.43900001,0.0160000008} +34 4 22 16365150 48.5699997 47 {1,1,0.999000013,0.998000026,0.990999997,0.972000003,0.906000018,0.381999999,0.0130000003} +35 4 22 16365160 46.7400017 45 {1,1,0.999000013,0.996999979,0.99000001,0.959999979,0.882000029,0.328999996,0.0109999999} +36 4 22 16365170 44.5999985 43 {1,1,0.999000013,0.998000026,0.987999976,0.944000006,0.848999977,0.272000015,0.00600000005} +37 4 22 16365180 43.0800018 41 {1,1,0.999000013,0.998000026,0.985000014,0.934000015,0.833999991,0.233999997,0.00600000005} +38 4 22 16365190 41.6399994 40 {1,1,0.999000013,0.995999992,0.978999972,0.907000005,0.81400001,0.197999999,0.00499999989} +39 4 22 16365200 40.1300011 39 {1,1,0.999000013,0.994000018,0.970000029,0.89200002,0.778999984,0.164000005,0.00400000019} +40 4 22 16365210 38.9599991 37 {1,1,0.999000013,0.991999984,0.954999983,0.883000016,0.751999974,0.145999998,0.00300000003} +41 4 22 16365220 38.3100014 36 {1,1,0.999000013,0.990999997,0.957000017,0.870000005,0.735000014,0.147,0.00200000009} +42 4 22 16365230 38.1599998 36 {1,1,0.999000013,0.990999997,0.952000022,0.859000027,0.731999993,0.140000001,0.00100000005} +43 4 22 16365240 37.9700012 36 {1,1,0.999000013,0.986999989,0.949999988,0.853999972,0.707000017,0.141000003,0.00200000009} +44 4 22 16365250 37.7999992 36 {1,1,0.999000013,0.987999976,0.939999998,0.848999977,0.698000014,0.136000007,0.00200000009} +45 4 22 16365260 37.6599998 36 {1,1,0.998000026,0.984000027,0.940999985,0.847000003,0.685000002,0.138999999,0.00200000009} +46 4 22 16365270 36.6899986 35 {1,1,0.998000026,0.980000019,0.926999986,0.824999988,0.657000005,0.123000003,0.00200000009} +47 4 22 16365280 35.5400009 34 {1,0.999000013,0.998000026,0.975000024,0.912,0.790000021,0.611999989,0.108999997,0.00200000009} +48 4 22 16365290 34.6699982 33 {1,0.999000013,0.996999979,0.972000003,0.903999984,0.768999994,0.577000022,0.100000001,0.00200000009} +49 4 22 16365300 36.3600006 35 {1,0.999000013,0.996999979,0.980000019,0.925000012,0.81099999,0.643999994,0.120999999,0.00200000009} +50 4 22 16365310 37.7299995 36 {1,0.999000013,0.998000026,0.985000014,0.944000006,0.842999995,0.67900002,0.144999996,0.00300000003} +51 4 22 16365320 39.0499992 37 {1,1,0.998000026,0.986999989,0.95599997,0.866999984,0.722000003,0.166999996,0.00499999989} +52 4 22 16365330 40.2200012 38 {1,1,0.996999979,0.991999984,0.959999979,0.873000026,0.744000018,0.196999997,0.00400000019} +53 4 22 16365340 41.9099998 40 {1,1,0.998000026,0.994000018,0.972000003,0.898000002,0.787999988,0.231999993,0.00600000005} +54 4 22 16365350 43.4599991 41 {1,1,0.999000013,0.995000005,0.971000016,0.925000012,0.819000006,0.270000011,0.00600000005} +55 4 22 16365360 45.8699989 44 {1,1,0.999000013,0.995999992,0.981999993,0.939999998,0.851999998,0.337000012,0.00600000005} +56 4 22 16365370 47.3699989 45.5 {1,1,0.999000013,0.995999992,0.989000022,0.952000022,0.876999974,0.36500001,0.0109999999} +57 4 22 16365380 49.7299995 47 {1,1,1,0.996999979,0.99000001,0.968999982,0.898000002,0.426999986,0.0130000003} +58 4 22 16365390 51.8600006 50 {1,1,1,0.998000026,0.995000005,0.97299999,0.925999999,0.479999989,0.0179999992} +59 4 22 16365400 53.5900002 51 {1,1,1,0.999000013,0.994000018,0.984000027,0.935000002,0.519999981,0.0250000004} +60 4 22 16365410 55.3699989 53 {1,1,1,0.999000013,0.995999992,0.986000001,0.949000001,0.555999994,0.0270000007} +61 4 22 16365420 57.9099998 55 {1,1,1,0.999000013,0.996999979,0.987999976,0.958999991,0.595000029,0.0350000001} +62 4 22 16365430 60.0200005 56 {1,1,1,1,0.996999979,0.989000022,0.968999982,0.630999982,0.0430000015} +63 4 22 16365440 61.5299988 58 {1,1,1,1,0.998000026,0.99000001,0.976999998,0.662,0.0489999987} +64 4 22 16365450 62.5600014 59 {1,1,1,1,0.998000026,0.990999997,0.977999985,0.675999999,0.0549999997} +65 4 22 16365460 63.8800011 60 {1,1,1,1,0.999000013,0.994000018,0.977999985,0.690999985,0.0700000003} +66 4 22 16365470 65.4899979 61.5 {1,1,1,1,0.999000013,0.995999992,0.976000011,0.70599997,0.0799999982} +67 4 22 16365480 66.2099991 62 {1,1,1,1,0.999000013,0.996999979,0.976999998,0.717999995,0.0879999995} +68 4 22 16365490 67.1200027 63 {1,1,1,1,0.999000013,0.994000018,0.977999985,0.72299999,0.0920000002} +69 4 22 16365500 68.4899979 64 {1,1,1,1,0.999000013,0.994000018,0.977999985,0.734000027,0.109999999} +70 4 22 16365510 69.0500031 64 {1,1,1,1,0.999000013,0.990999997,0.976999998,0.739000022,0.119999997} +71 4 22 16365520 68.9100037 64 {1,1,1,1,0.999000013,0.992999971,0.975000024,0.737999976,0.123999998} +72 4 22 16365530 68.3099976 63 {1,1,1,1,0.999000013,0.987999976,0.976000011,0.712000012,0.120999999} +73 4 22 16365540 68.0599976 63 {1,1,1,0.999000013,0.998000026,0.987999976,0.972000003,0.708999991,0.116999999} +74 4 22 16365550 68.5199966 63 {1,1,1,0.999000013,0.998000026,0.987999976,0.972000003,0.714999974,0.122000001} +75 4 22 16365560 68.1200027 63 {1,1,1,0.999000013,0.998000026,0.987999976,0.964999974,0.714999974,0.120999999} +76 4 22 16365570 68.4400024 64 {1,1,1,0.999000013,0.995999992,0.985000014,0.963999987,0.716000021,0.123999998} +77 4 22 16365580 70.0800018 64 {1,1,1,0.998000026,0.996999979,0.989000022,0.970000029,0.723999977,0.141000003} +78 4 22 16365590 70.9899979 65.5 {1,1,1,0.999000013,0.996999979,0.992999971,0.978999972,0.739000022,0.148000002} +79 4 22 16365600 71.7099991 67 {1,1,1,0.999000013,0.996999979,0.995000005,0.981999993,0.769999981,0.151999995} +80 4 22 16365610 72.9400024 68 {1,1,1,0.999000013,0.998000026,0.995000005,0.986999989,0.795000017,0.153999999} +81 4 22 16365620 73.3099976 68 {1,1,1,1,0.999000013,0.995000005,0.986000001,0.79400003,0.158999994} +82 4 22 16365630 74.3000031 69 {1,1,1,1,0.999000013,0.995000005,0.986999989,0.792999983,0.158000007} +83 4 22 16365640 74.8099976 69 {1,1,1,1,0.998000026,0.995000005,0.986000001,0.791000009,0.166999996} +84 4 22 16365650 74.6299973 69 {1,1,1,1,0.999000013,0.995000005,0.985000014,0.790000021,0.163000003} +85 4 22 16365660 74.7200012 69 {1,1,1,1,0.999000013,0.995999992,0.985000014,0.796000004,0.160999998} +86 4 22 16365670 75.9899979 70 {1,1,1,1,0.999000013,0.995999992,0.985000014,0.808000028,0.173999995} +87 4 22 16365680 76.4499969 71 {1,1,1,1,0.999000013,0.998000026,0.986000001,0.816999972,0.180999994} +88 4 22 16365690 76.4899979 71 {1,1,1,1,0.999000013,0.999000013,0.986999989,0.811999977,0.182999998} +89 4 22 16365700 76.3199997 71 {1,1,1,1,0.999000013,0.998000026,0.986999989,0.811999977,0.180000007} +90 4 22 16365710 76.6200027 70 {1,1,1,1,0.999000013,0.999000013,0.987999976,0.82099998,0.184} +91 4 22 16365720 76.1500015 70 {1,1,1,1,0.999000013,0.998000026,0.99000001,0.810000002,0.186000004} +92 4 22 16365730 75.1900024 69 {1,1,1,1,0.999000013,0.995999992,0.986000001,0.808000028,0.171000004} +93 4 22 16365740 74.25 68 {1,1,1,1,0.999000013,0.996999979,0.98299998,0.781000018,0.166999996} +94 4 22 16365750 73.1699982 67.5 {1,1,1,1,0.998000026,0.991999984,0.977999985,0.764999986,0.153999999} +95 4 22 16365760 72.3499985 66 {1,1,1,1,0.995999992,0.987999976,0.970000029,0.746999979,0.155000001} +96 4 22 16365770 72.1600037 67 {1,1,1,0.999000013,0.995999992,0.987999976,0.976999998,0.742999971,0.158999994} +97 4 22 16365780 72.3199997 67 {1,1,1,0.999000013,0.996999979,0.991999984,0.976999998,0.762000024,0.158999994} +98 4 22 16365790 72.3700027 67 {1,1,1,1,0.996999979,0.992999971,0.980000019,0.764999986,0.155000001} +99 4 22 16365800 73.0400009 68 {1,1,1,1,0.999000013,0.995000005,0.980000019,0.781000018,0.153999999} +100 4 22 16365810 73.6100006 69 {1,1,1,1,1,0.995999992,0.985000014,0.805999994,0.158000007} +101 4 22 16365820 73.3799973 69 {1,1,1,1,1,0.998000026,0.986000001,0.808000028,0.150000006} 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{1,1,1,0.999000013,0.992999971,0.947000027,0.815999985,0.115999997,0.00100000005} +489 4 22 46615780 38.5099983 37 {1,1,1,1,0.991999984,0.93900001,0.809000015,0.111000001,0.00100000005} +490 4 22 46615790 38.4599991 37 {1,1,1,1,0.995000005,0.940999985,0.808000028,0.108999997,0.00100000005} +491 4 22 46615800 38.1500015 36 {1,1,1,1,0.995000005,0.941999972,0.790000021,0.107000001,0.00100000005} +492 4 22 46615810 37.9700012 36 {1,1,1,1,0.995000005,0.935000002,0.787,0.104000002,0.00100000005} +493 4 22 46615820 38.0900002 36 {1,1,1,0.999000013,0.991999984,0.938000023,0.792999983,0.101000004,0.00100000005} +494 4 22 46615830 38.7099991 37 {1,1,1,0.999000013,0.990999997,0.944999993,0.810000002,0.104000002,0.00100000005} +495 4 22 46615840 39.3499985 37 {1,1,1,1,0.994000018,0.958000004,0.837000012,0.123999998,0.00100000005} +496 4 22 46615850 40.0699997 38 {1,1,1,0.998000026,0.995999992,0.968999982,0.860000014,0.137999997,0.00100000005} +497 4 22 46615860 40.3499985 39 {1,1,1,1,0.995999992,0.976000011,0.865999997,0.140000001,0.00100000005} +498 4 22 46615870 40.2799988 39 {1,1,1,1,0.996999979,0.970000029,0.85799998,0.131999999,0.00100000005} +499 4 22 46615880 40.3199997 39 {1,1,1,1,0.995000005,0.971000016,0.855000019,0.138999999,0} +500 4 22 46615890 40.5800018 39 {1,1,1,0.999000013,0.996999979,0.970000029,0.864000022,0.152999997,0.00100000005} +501 4 22 46615900 40.1800003 38 {1,1,1,1,0.995000005,0.972000003,0.852999985,0.136999995,0.00100000005} +502 4 22 46615910 39.7599983 38 {1,1,1,1,0.995000005,0.961000025,0.845000029,0.125,0.00100000005} +503 4 22 46615920 39.1100006 37 {1,1,1,1,0.994000018,0.953999996,0.832000017,0.116999999,0} +504 4 22 46615930 38.75 37 {1,1,1,1,0.994000018,0.954999983,0.819999993,0.104999997,0.00100000005} +\. + +COPY data.genes (id, reference_set, gene_id, gene_name, full_name, canonical_transcript, chrom, start_pos, end_pos, strand) FROM stdin; +1 1 ENSG00000228314 CYP4F29P cytochrome P450, family 4, subfamily F, polypeptide 29, pseudogene ENST00000428301 21 15215454 15220685 - +2 1 ENSG00000183249 NF1P3 neurofibromin 1 pseudogene 3 ENST00000457709 21 15373248 15377600 + +3 1 ENSG00000238197 PAXBP1-AS1 \N ENST00000440052 21 34100426 34115433 + +4 1 ENSG00000159086 PAXBP1 PAX3 and PAX7 binding protein 1 ENST00000331923 21 34106210 34144169 - +5 1 ENSG00000233866 LA16c-4G1.3 \N ENST00000424770 22 16062157 16063236 + +6 1 ENSG00000229286 LA16c-4G1.4 \N ENST00000448070 22 16076052 16076172 - +7 1 ENSG00000235265 LA16c-4G1.5 \N ENST00000413156 22 16084249 16084826 - +8 1 ENSG00000223875 NBEAP3 neurobeachin pseudogene 3 ENST00000420638 22 16100517 16124973 - +9 1 ENSG00000215270 LA16c-60H5.7 \N ENST00000398242 22 16122720 16123768 + +10 1 ENSG00000241838 LA16c-3G11.7 \N ENST00000417657 22 16255355 16256477 - +11 1 ENSG00000198062 POTEH POTE ankyrin domain family, member H ENST00000343518 22 16256441 16287937 - +12 1 ENSG00000236666 POTEH-AS1 \N ENST00000422014 22 16274560 16278602 + +13 1 ENSG00000212216 RNU6-816P \N ENST00000390914 22 16276398 16276504 - +14 1 ENSG00000224435 NF1P6 neurofibromin 1 pseudogene 6 ENST00000426025 22 16345912 16355362 + +15 1 ENSG00000226474 LA16c-2F2.5 \N ENST00000440999 22 16362385 16362561 + +16 1 ENSG00000231565 NEK2P2 NEK2 pseudogene 2 ENST00000438441 22 16364867 16366204 + +17 1 ENSG00000230471 LA16c-2F2.8 \N ENST00000428118 22 16373081 16377055 + +18 1 ENSG00000229658 PABPC1P9 poly(A) binding protein, cytoplasmic 1 pseudogene 9 ENST00000426076 22 16904668 16906756 + +19 1 ENSG00000226444 ACTR3BP6 ACTR3B pseudogene 6 ENST00000421366 22 16967410 16969212 + +20 1 ENSG00000249263 PARP4P3 poly (ADP-ribose) polymerase family, member 4 pseudogene 3 ENST00000510265 22 17134782 17140518 - +21 1 ENSG00000189295 ANKRD62P1-PARP4P3 \N ENST00000338526 22 17134956 17160374 - +22 1 ENSG00000015475 BID BH3 interacting domain death agonist ENST00000317361 22 18216906 18257536 - +23 1 ENSG00000251940 SNORA15 \N ENST00000516131 22 19237396 19237489 + +24 1 ENSG00000100053 CRYBB3 crystallin, beta B3 ENST00000215855 22 25595817 25603330 + +25 1 ENSG00000236641 CTA-221G9.7 \N ENST00000454253 22 25608709 25609652 + +26 1 ENSG00000244752 CRYBB2 crystallin, beta B2 ENST00000398215 22 25615489 25627836 + +27 1 ENSG00000100249 C22orf31 \N ENST00000216071 22 29454660 29457832 - +28 1 ENSG00000100105 PATZ1 POZ (BTB) and AT hook containing zinc finger 1 ENST00000266269 22 31721790 31742218 - +29 1 ENSG00000100156 SLC16A8 solute carrier family 16 (monocarboxylate transporter), member 8 ENST00000320521 22 38474141 38480100 - +30 1 ENSG00000128298 BAIAP2L2 BAI1-associated protein 2-like 2 ENST00000381669 22 38480896 38506677 - +31 1 ENSG00000272720 CTA-228A9.3 \N ENST00000609162 22 38486134 38487566 + +32 1 ENSG00000100266 PACSIN2 protein kinase C and casein kinase substrate in neurons 2 ENST00000263246 22 43231418 43411151 - +33 1 ENSG00000188677 PARVB parvin, beta ENST00000406477 22 44395091 44568829 + +34 1 ENSG00000138964 PARVG parvin, gamma ENST00000444313 22 44568836 44615413 + +35 1 ENSG00000186951 PPARA peroxisome proliferator-activated receptor alpha ENST00000396000 22 46546424 46639653 + +36 1 ENSG00000073150 PANX2 pannexin 2 ENST00000395842 22 50609160 50618723 + +\. + +COPY data.transcripts (id, transcript_id, gene, mim_annotation, mim_gene_accession, chrom, start_pos, stop_pos, strand) FROM stdin; +1 ENST00000428301 1 \N \N 21 15215454 15220685 - +2 ENST00000420685 1 \N \N 21 15219080 15220034 - +3 ENST00000436765 1 \N \N 21 15219080 15220526 - +4 ENST00000457709 2 \N \N 21 15373248 15377600 + +5 ENST00000458479 3 \N \N 21 34100426 34105227 + +6 ENST00000440052 3 \N \N 21 34100450 34115433 + +7 ENST00000455170 3 \N \N 21 34102663 34109784 + +8 ENST00000331923 4 \N \N 21 34106210 34144169 - +9 ENST00000466846 4 \N \N 21 34106211 34129105 - +10 ENST00000443785 4 \N \N 21 34107131 34143998 - +11 ENST00000497873 4 \N \N 21 34107137 34124435 - +12 ENST00000290178 4 \N \N 21 34113704 34143979 - +13 ENST00000445049 4 \N \N 21 34113730 34115579 - +14 ENST00000421049 4 \N \N 21 34120870 34127622 - +15 ENST00000472588 4 \N \N 21 34128653 34143979 - +16 ENST00000464256 4 \N \N 21 34131713 34144103 - +17 ENST00000424770 5 \N \N 22 16062157 16063236 + +18 ENST00000448070 6 \N \N 22 16076052 16076172 - +19 ENST00000413156 7 \N \N 22 16084249 16084826 - +20 ENST00000420638 8 \N \N 22 16100517 16124973 - +21 ENST00000398242 9 \N \N 22 16122720 16123768 + +22 ENST00000417657 10 \N \N 22 16255355 16256477 - +23 ENST00000339523 10 \N \N 22 16255919 16256227 - +24 ENST00000452800 11 \N \N 22 16256441 16287717 - +25 ENST00000343518 11 \N \N 22 16256441 16287937 - +26 ENST00000422014 12 \N \N 22 16274560 16278602 + +27 ENST00000390914 13 \N \N 22 16276398 16276504 - +28 ENST00000426025 14 \N \N 22 16345912 16355362 + +29 ENST00000440999 15 \N \N 22 16362385 16362561 + +30 ENST00000438441 16 \N \N 22 16364867 16366204 + +31 ENST00000428118 17 \N \N 22 16373081 16377055 + +32 ENST00000426076 18 \N \N 22 16904668 16906756 + +33 ENST00000422332 19 \N \N 22 16967410 16968778 + +34 ENST00000421366 19 \N \N 22 16967893 16969212 + +35 ENST00000510265 20 \N \N 22 17134782 17140518 - +36 ENST00000456726 21 \N \N 22 17134956 17156430 - +37 ENST00000457060 21 \N \N 22 17150354 17156342 - +38 ENST00000338526 21 \N \N 22 17154451 17160374 - +39 ENST00000317361 22 \N \N 22 18216906 18256782 - +40 ENST00000399767 22 \N \N 22 18216908 18257258 - +41 ENST00000399774 22 \N \N 22 18216937 18257258 - +42 ENST00000399765 22 \N \N 22 18216941 18257255 - +43 ENST00000494097 22 \N \N 22 18217988 18223960 - +44 ENST00000342111 22 \N \N 22 18218265 18257178 - +45 ENST00000550946 22 \N \N 22 18218318 18257178 - +46 ENST00000551952 22 \N \N 22 18218318 18257431 - +47 ENST00000473439 22 \N \N 22 18220824 18257261 - +48 ENST00000552886 22 \N \N 22 18222214 18257536 - +49 ENST00000516131 23 \N \N 22 19237396 19237489 + +50 ENST00000215855 24 \N \N 22 25595817 25603330 + +51 ENST00000404334 24 \N \N 22 25595840 25603234 + +52 ENST00000454253 25 \N \N 22 25608709 25609652 + +53 ENST00000398215 26 \N \N 22 25615489 25627836 + +54 ENST00000216071 27 \N \N 22 29454660 29457832 - +55 ENST00000266269 28 \N \N 22 31721790 31742218 - +56 ENST00000405309 28 \N \N 22 31721795 31742218 - +57 ENST00000351933 28 \N \N 22 31721795 31742218 - +58 ENST00000494109 28 \N \N 22 31731404 31739271 - +59 ENST00000465287 28 \N \N 22 31736663 31739577 - +60 ENST00000215919 28 \N \N 22 31736663 31741762 - +61 ENST00000320521 29 \N \N 22 38474141 38479149 - +62 ENST00000469516 29 \N \N 22 38474141 38480100 - +63 ENST00000427592 29 \N \N 22 38477962 38480100 - +64 ENST00000381669 30 \N \N 22 38480896 38506677 - +65 ENST00000428572 30 \N \N 22 38481172 38484945 - +66 ENST00000332536 30 \N \N 22 38489921 38506676 - +67 ENST00000609162 31 \N \N 22 38486134 38487566 + +68 ENST00000507586 32 \N \N 22 43231418 43272213 - +69 ENST00000263246 32 \N \N 22 43265777 43411151 - +70 ENST00000337959 32 \N \N 22 43265777 43411151 - +71 ENST00000407585 32 \N \N 22 43265781 43355887 - +72 ENST00000403744 32 \N \N 22 43266936 43343047 - +73 ENST00000402229 32 \N \N 22 43267134 43355884 - +74 ENST00000453643 32 \N \N 22 43286941 43411141 - +75 ENST00000418133 32 \N \N 22 43286950 43341879 - +76 ENST00000422336 32 \N \N 22 43286950 43398446 - +77 ENST00000445706 32 \N \N 22 43289463 43411104 - +78 ENST00000453079 32 \N \N 22 43289580 43355905 - +79 ENST00000406477 33 \N \N 22 44395091 44564803 + +80 ENST00000338758 33 \N \N 22 44420157 44568829 + +81 ENST00000402876 33 \N \N 22 44420182 44515814 + +82 ENST00000444029 33 \N \N 22 44427245 44528845 + +83 ENST00000404989 33 \N \N 22 44464941 44565064 + +84 ENST00000477795 33 \N \N 22 44482564 44495969 + +85 ENST00000495824 33 \N \N 22 44532344 44535004 + +86 ENST00000484345 33 \N \N 22 44558614 44564123 + +87 ENST00000477438 33 \N \N 22 44564059 44564807 + +88 ENST00000422871 34 \N \N 22 44568836 44603034 + +89 ENST00000453888 34 \N \N 22 44568864 44583052 + +90 ENST00000444313 34 \N \N 22 44576770 44604349 + +91 ENST00000416291 34 \N \N 22 44576902 44579288 + +92 ENST00000475485 34 \N \N 22 44577216 44602502 + +93 ENST00000415224 34 \N \N 22 44577257 44603034 + +94 ENST00000417767 34 \N \N 22 44577278 44579299 + +95 ENST00000356909 34 \N \N 22 44577280 44602515 + +96 ENST00000471836 34 \N \N 22 44577630 44581994 + +97 ENST00000466375 34 \N \N 22 44577741 44580141 + +98 ENST00000468564 34 \N \N 22 44581406 44603035 + +99 ENST00000472551 34 \N \N 22 44591978 44615413 + +100 ENST00000440343 35 \N \N 22 46546424 46594307 + +101 ENST00000415785 35 \N \N 22 46546455 46594488 + +102 ENST00000396000 35 \N \N 22 46546499 46639653 + +103 ENST00000262735 35 \N \N 22 46546499 46639653 + +104 ENST00000420804 35 \N \N 22 46546509 46611261 + +105 ENST00000460086 35 \N \N 22 46546731 46547873 + +106 ENST00000407236 35 \N \N 22 46547787 46639652 + +107 ENST00000496865 35 \N \N 22 46547789 46552488 + +108 ENST00000484619 35 \N \N 22 46567183 46594307 + +109 ENST00000481567 35 \N \N 22 46567231 46594307 + +110 ENST00000402126 35 \N \N 22 46572645 46631300 + +111 ENST00000493286 35 \N \N 22 46572663 46616554 + +112 ENST00000434345 35 \N \N 22 46594281 46631277 + +113 ENST00000159647 36 \N \N 22 50609160 50618721 + +114 ENST00000395842 36 \N \N 22 50609160 50618723 + +115 ENST00000402472 36 \N \N 22 50609190 50618027 + +\. + +COPY data.features (id, gene, transcript, chrom, start_pos, stop_pos, strand, feature_type) FROM stdin; +1 1 1 21 15220411 15220685 - exon +2 1 1 21 15219080 15219270 - exon +3 1 1 21 15218334 15218462 - exon +4 1 1 21 15217326 15217595 - exon +5 1 1 21 15216343 15216456 - exon +6 1 1 21 15215454 15215753 - exon +7 1 2 21 15219771 15220034 - exon +8 1 2 21 15219384 15219444 - exon +9 1 2 21 15219080 15219200 - exon +10 1 3 21 15220411 15220526 - exon +11 1 3 21 15219771 15219913 - exon +12 1 3 21 15219080 15219444 - exon +13 2 4 21 15373248 15373421 + exon +14 2 4 21 15373863 15373983 + exon +15 2 4 21 15374231 15374305 + exon +16 2 4 21 15377521 15377600 + exon +17 3 5 21 34100426 34102972 + exon +18 3 5 21 34104830 34105227 + exon +19 3 6 21 34100450 34102972 + exon +20 3 6 21 34105900 34105968 + exon +21 3 6 21 34110583 34110652 + exon +22 3 6 21 34114573 34115433 + exon +23 3 7 21 34102663 34102972 + exon +24 3 7 21 34105900 34105968 + exon +25 3 7 21 34109684 34109784 + exon +26 4 8 21 34143637 34144169 - exon +27 4 8 21 34143637 34143979 - CDS +28 4 8 21 34142125 34142253 - exon +29 4 8 21 34142125 34142253 - CDS +30 4 8 21 34136659 34136835 - exon +31 4 8 21 34136659 34136835 - CDS +32 4 8 21 34134407 34134628 - exon +33 4 8 21 34134407 34134628 - CDS +34 4 8 21 34133370 34133473 - exon +35 4 8 21 34133370 34133473 - CDS +36 4 8 21 34132088 34132305 - exon +37 4 8 21 34132088 34132305 - CDS +38 4 8 21 34131391 34131580 - exon +39 4 8 21 34131391 34131580 - CDS +40 4 8 21 34127541 34127664 - exon +41 4 8 21 34127541 34127664 - CDS +42 4 8 21 34123430 34123529 - exon +43 4 8 21 34123430 34123529 - CDS +44 4 8 21 34123228 34123343 - exon +45 4 8 21 34123228 34123343 - CDS +46 4 8 21 34120810 34121009 - exon +47 4 8 21 34120810 34121009 - CDS +48 4 8 21 34117885 34118029 - exon +49 4 8 21 34117885 34118029 - CDS +50 4 8 21 34117103 34117224 - exon +51 4 8 21 34117103 34117224 - CDS +52 4 8 21 34115989 34116065 - exon +53 4 8 21 34115989 34116065 - CDS +54 4 8 21 34115559 34115625 - exon +55 4 8 21 34115559 34115625 - CDS +56 4 8 21 34110484 34110630 - exon +57 4 8 21 34110484 34110630 - CDS +58 4 8 21 34109565 34109719 - exon +59 4 8 21 34109565 34109719 - CDS +60 4 8 21 34106210 34107378 - exon +61 4 8 21 34107264 34107378 - CDS +62 4 8 21 34143980 34144169 - UTR +63 4 8 21 34106210 34107263 - UTR +64 4 9 21 34127524 34129105 - exon +65 4 9 21 34123430 34123529 - exon +66 4 9 21 34123228 34123343 - exon +67 4 9 21 34120810 34121009 - exon +68 4 9 21 34117885 34118029 - exon +69 4 9 21 34117103 34117224 - exon +70 4 9 21 34115989 34116065 - exon +71 4 9 21 34115559 34115625 - exon +72 4 9 21 34110484 34110630 - exon +73 4 9 21 34109565 34109719 - exon +74 4 9 21 34106211 34107378 - exon +75 4 10 21 34143637 34143998 - exon +76 4 10 21 34143637 34143979 - CDS +77 4 10 21 34142125 34142253 - exon +78 4 10 21 34142125 34142253 - CDS +79 4 10 21 34136659 34136835 - exon +80 4 10 21 34136659 34136835 - CDS +81 4 10 21 34134407 34134628 - exon +82 4 10 21 34134407 34134628 - CDS +83 4 10 21 34133370 34133473 - exon +84 4 10 21 34133370 34133473 - CDS +85 4 10 21 34132088 34132305 - exon +86 4 10 21 34132088 34132305 - CDS +87 4 10 21 34131391 34131580 - exon +88 4 10 21 34131391 34131580 - CDS +89 4 10 21 34127524 34127664 - exon +90 4 10 21 34127524 34127664 - CDS +91 4 10 21 34123430 34123529 - exon +92 4 10 21 34123521 34123529 - CDS +93 4 10 21 34123228 34123343 - exon +94 4 10 21 34120810 34121009 - exon +95 4 10 21 34117885 34118029 - exon +96 4 10 21 34117103 34117224 - exon +97 4 10 21 34115989 34116065 - exon +98 4 10 21 34115559 34115625 - exon +99 4 10 21 34110484 34110630 - exon +100 4 10 21 34109565 34109719 - exon +101 4 10 21 34107131 34107378 - exon +102 4 10 21 34143980 34143998 - UTR +103 4 10 21 34123430 34123520 - UTR +104 4 10 21 34123228 34123343 - UTR +105 4 10 21 34120810 34121009 - UTR +106 4 10 21 34117885 34118029 - UTR +107 4 10 21 34117103 34117224 - UTR +108 4 10 21 34115989 34116065 - UTR +109 4 10 21 34115559 34115625 - UTR +110 4 10 21 34110484 34110630 - UTR +111 4 10 21 34109565 34109719 - UTR +112 4 10 21 34107131 34107378 - UTR +113 4 11 21 34123430 34124435 - exon +114 4 11 21 34123228 34123343 - exon +115 4 11 21 34120810 34121009 - exon +116 4 11 21 34117885 34118029 - exon +117 4 11 21 34117103 34117224 - exon +118 4 11 21 34115989 34116065 - exon +119 4 11 21 34115559 34115625 - exon +120 4 11 21 34110484 34110630 - exon +121 4 11 21 34109565 34109719 - exon +122 4 11 21 34107137 34107378 - exon +123 4 12 21 34143637 34143979 - exon +124 4 12 21 34143637 34143979 - CDS +125 4 12 21 34142125 34142253 - exon +126 4 12 21 34142125 34142253 - CDS +127 4 12 21 34136659 34136835 - exon +128 4 12 21 34136659 34136835 - CDS +129 4 12 21 34134407 34134628 - exon +130 4 12 21 34134407 34134628 - CDS +131 4 12 21 34133370 34133473 - exon +132 4 12 21 34133370 34133473 - CDS +133 4 12 21 34132088 34132305 - exon +134 4 12 21 34132088 34132305 - CDS +135 4 12 21 34131391 34131580 - exon +136 4 12 21 34131391 34131580 - CDS +137 4 12 21 34127541 34127664 - exon +138 4 12 21 34127541 34127664 - CDS +139 4 12 21 34123430 34123529 - exon +140 4 12 21 34123430 34123529 - CDS +141 4 12 21 34123228 34123343 - exon +142 4 12 21 34123228 34123343 - CDS +143 4 12 21 34120810 34121009 - exon +144 4 12 21 34120810 34121009 - CDS +145 4 12 21 34117885 34118029 - exon +146 4 12 21 34117885 34118029 - CDS +147 4 12 21 34117103 34117224 - exon +148 4 12 21 34117103 34117224 - CDS +149 4 12 21 34115989 34116065 - exon +150 4 12 21 34115989 34116065 - CDS +151 4 12 21 34115559 34115625 - exon +152 4 12 21 34115559 34115625 - CDS +153 4 12 21 34113704 34113933 - exon +154 4 12 21 34113823 34113933 - CDS +155 4 12 21 34113704 34113822 - UTR +156 4 13 21 34115559 34115579 - exon +157 4 13 21 34115559 34115579 - CDS +158 4 13 21 34115272 34115377 - exon +159 4 13 21 34115324 34115377 - CDS +160 4 13 21 34114671 34114812 - exon +161 4 13 21 34113730 34113933 - exon +162 4 13 21 34115272 34115323 - UTR +163 4 13 21 34114671 34114812 - UTR +164 4 13 21 34113730 34113933 - UTR +165 4 14 21 34127524 34127622 - exon +166 4 14 21 34127524 34127622 - CDS +167 4 14 21 34123430 34123529 - exon +168 4 14 21 34123521 34123529 - CDS +169 4 14 21 34120870 34121009 - exon +170 4 14 21 34123430 34123520 - UTR +171 4 14 21 34120870 34121009 - UTR +172 4 15 21 34143637 34143979 - exon +173 4 15 21 34142125 34142253 - exon +174 4 15 21 34136659 34136835 - exon +175 4 15 21 34134407 34134628 - exon +176 4 15 21 34133370 34133473 - exon +177 4 15 21 34132088 34132305 - exon +178 4 15 21 34131391 34131580 - exon 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113 22 50617687 50618721 + UTR +1158 36 114 22 50609160 50609385 + exon +1159 36 114 22 50609160 50609385 + CDS +1160 36 114 22 50615368 50616831 + exon +1161 36 114 22 50615368 50616831 + CDS +1162 36 114 22 50617363 50618723 + exon +1163 36 114 22 50617363 50617703 + CDS +1164 36 114 22 50617704 50618723 + UTR +1165 36 115 22 50609190 50609385 + exon +1166 36 115 22 50609190 50609385 + CDS +1167 36 115 22 50613861 50613911 + exon +1168 36 115 22 50613861 50613895 + CDS +1169 36 115 22 50615368 50616831 + exon +1170 36 115 22 50617363 50617564 + exon +1171 36 115 22 50617650 50618027 + exon +1172 36 115 22 50613896 50613911 + UTR +1173 36 115 22 50615368 50616831 + UTR +1174 36 115 22 50617363 50617564 + UTR +1175 36 115 22 50617650 50618027 + UTR +\. + +COPY data.gene_other_names (id, gene, name) FROM stdin; +1 1 CYP4F-se4[6:7:8] +2 4 GCFC +3 4 fSAP105 +4 8 BCL8C +5 11 POTE22 +6 11 CT104.7 +7 14 Em:AP000532.C22.1 +8 28 MAZR +9 28 dJ400N23 +10 28 ZBTB19 +11 28 ZSG +12 28 RIAZ +13 28 PATZ +14 29 MCT3 +15 29 REMP +16 30 FLJ22582 +17 32 SDPII +18 33 CGI-56 +19 35 hPPAR +20 35 NR1C1 +21 36 hPANX2 +22 36 PX2 +\. + +COPY data.sample_sets (id, dataset, collection, sample_size, phenotype) FROM stdin; +1 1 1 0 Undefined +\. + +COPY data.variants (id, dataset_version, variant_type, rsid, chrom, pos, ref, alt, site_quality, orig_alt_alleles, hom_count, allele_freq, filter_string, variant_id, allele_count, allele_num, quality_metrics, vep_annotations) FROM stdin; +2 1 \N 76676778 21 9411609 G T 851236 {21-9411609-G-T} 10 0.384769529 VQSRTrancheSNP99.00to99.90 21-9411609-G-T 768 1996 {"DP": "70984", "FS": "0", "MQ": "55.26", "QD": "14.21", "VQSLOD": "-9.25", "MQRankSum": "0.131", "BaseQRankSum": "-0.574", "ReadPosRankSum": "0.568", "ClippingRankSum": "-0.047"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "T", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "", "SYMBOL": "", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intergenic_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs76676778", "MOTIF_SCORE_CHANGE": ""}] +5 4 \N 201064279 22 16079227 C T 113238 {22-16079227-C-T} 558 0.559284091 VQSRTrancheSNP99.90to100.00 22-16079227-C-T 1000 1788 {"DP": "7287", "FS": "0", "MQ": "25.51", "QD": "17.74", "VQSLOD": "-62.34", "MQRankSum": "-1.92", "BaseQRankSum": "0.72", "ReadPosRankSum": "0.358", "ClippingRankSum": "0.289"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000229286", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "T", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-4G1.4", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "unprocessed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000448070", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "3055", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs62225771", "MOTIF_SCORE_CHANGE": ""}] +7 4 \N 199594940 22 16079289 A G 86684.8984 {22-16079289-A-G} 374 0.462406009 VQSRTrancheSNP99.90to100.00 22-16079289-A-G 861 1862 {"DP": "7725", "FS": "0", "MQ": "25.51", "QD": "14.12", "VQSLOD": "-55.69", "MQRankSum": "-1.286", "BaseQRankSum": "-1.739", "ReadPosRankSum": "0.678", "ClippingRankSum": "0.198"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000229286", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "G", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-4G1.4", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "unprocessed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000448070", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "3117", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs62225772", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000235265", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "G", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-4G1.5", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "unprocessed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000413156", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "4960", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs62225772", "MOTIF_SCORE_CHANGE": ""}] +9 4 \N 373706802 22 16080482 CAT C 117760 {22-16080482-CAT-C,22-16080482-C-CAT,22-16080482-C-CATACATATATATTGTATATGTAT} 8 0.157947689 PASS 22-16080482-CAT-C 314 1988 {"DP": "37043", "FS": "0", "MQ": "58.61", "QD": "10.1", "VQSLOD": "4.57", "MQRankSum": "0.052", "BaseQRankSum": "0.181", "ReadPosRankSum": "0", "ClippingRankSum": "0.017", "InbreedingCoeff": "-0.24"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000235265", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-4G1.5", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "unprocessed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000413156", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "3765", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs373706802", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000229286", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-4G1.4", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "unprocessed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000448070", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "4311", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs373706802", "MOTIF_SCORE_CHANGE": ""}] +12 4 \N \N 22 16251550 G A 3705.6001 {22-16251550-G-A} 0 0.0120000001 VQSRTrancheSNP99.90to100.00 22-16251550-G-A 24 2000 {"DP": "10381", "FS": "4.888", "MQ": "37.61", "QD": "11.09", "VQSLOD": "-28.51", "MQRankSum": "1.11", "BaseQRankSum": "0.849", "ReadPosRankSum": "0.572", "ClippingRankSum": "0.34", "InbreedingCoeff": "-0.0024"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "4891", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000241838", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-3G11.7", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "processed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000339523", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "4369", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "4891", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "", "EXON": "", "GMAF": "", "Gene": "ENSG00000241838", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "LA16c-3G11.7", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "processed_pseudogene", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000417657", "HGNC_ID": "", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "", "CLIN_SIG": "", "DISTANCE": "3805", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "downstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "Clone_based_vega_gene", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +13 4 \N \N 22 16251569 G A 2132.31006 {22-16251569-G-A} 2 0.0317220539 VQSRTrancheSNP99.90to100.00 22-16251569-G-A 63 1986 {"DP": "8327", "FS": "0", "MQ": "33.95", "QD": "4.14", "VQSLOD": "-38.48", "MQRankSum": "0.061", "BaseQRankSum": "-0.572", "ReadPosRankSum": "0", "ClippingRankSum": "-0.071", "InbreedingCoeff": "-0.0978"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", 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"Amino_acids": "", "Consequence": "intron_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +414 4 \N \N 22 16269420 AT A 12175.2002 {22-16269420-A-AT,22-16269420-ATTTTTT-A,22-16269420-ATTTTT-A,22-16269420-AT-A,22-16269420-ATTTT-A} 12 0.0121827414 PASS 22-16269420-AT-A 24 1970 {"DP": "23826", "FS": "9.214", "MQ": "40.78", "QD": "11.24", "VQSLOD": "-0.5967", "MQRankSum": "0.678", "BaseQRankSum": "-0.747", "ReadPosRankSum": "0.538", "ClippingRankSum": "0.067"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": 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"POTEH_HUMAN", "ALLELE_NUM": "4", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +417 4 \N \N 22 16269422 T * 9681.5498 {22-16269422-T-TC,22-16269422-T-*} 4 0.0267958958 PASS 22-16269422-T-* 47 1754 {"DP": "24970", "FS": "0", "MQ": "38.97", "QD": "13.43", "VQSLOD": "-1.049", "MQRankSum": "1.52", "BaseQRankSum": "0.747", "ReadPosRankSum": "0.747", "ClippingRankSum": "0.296", "InbreedingCoeff": "0.0863"} [] +418 4 \N 75875229 22 16269423 T C 60439 {22-16269423-T-C,22-16269423-T-*} 4 0.256830603 VQSRTrancheSNP99.00to99.90 22-16269423-T-C 470 1830 {"DP": "21134", "FS": "0", "MQ": "38.13", "QD": "6.62", "VQSLOD": "-23.76", "MQRankSum": "-1.626", "BaseQRankSum": "-0.545", "ReadPosRankSum": "-0.751", "ClippingRankSum": "0"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "ENST00000452800.1:c.*484+450A>G", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "C", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "8/11", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", 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"VARIANT_CLASS": "insertion", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +817 4 \N 142856307 22 16285954 TTATA T 565156 {22-16285954-TTATA-T,22-16285954-T-TTATA,22-16285954-T-TTTTATTTATA,22-16285954-TTA-T,22-16285954-T-TTATATATA,22-16285954-T-TTA} 80 0.321305841 PASS 22-16285954-TTATA-T 561 1746 {"DP": "39541", "FS": "0", "MQ": "58.41", "QD": "19.22", "VQSLOD": "-0.7886", "MQRankSum": "1.27", "BaseQRankSum": "-0.134", "ReadPosRankSum": "-0.653", "ClippingRankSum": "-0.036"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "-:0.2833", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "ENST00000343518.6:c.632+1296_632+1299delTATA", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "1/10", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "-:0.3517", "AMR_MAF": "-:0.2709", 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"ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs142856307", "MOTIF_SCORE_CHANGE": ""}] +818 4 \N 142856307 22 16285954 T TTATA 565156 {22-16285954-TTATA-T,22-16285954-T-TTATA,22-16285954-T-TTTTATTTATA,22-16285954-TTA-T,22-16285954-T-TTATATATA,22-16285954-T-TTA} 4 0.0366552137 PASS 22-16285954-T-TTATA 64 1746 {"DP": "39541", "FS": "0", "MQ": "58.41", "QD": "19.22", "VQSLOD": "-0.7886", "MQRankSum": "1.27", "BaseQRankSum": "-0.134", "ReadPosRankSum": "-0.653", "ClippingRankSum": "-0.036"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "-:0.2833", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "ENST00000343518.6:c.632+1296_632+1299dupTATA", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", 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"GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant&NMD_transcript_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs142856307", "MOTIF_SCORE_CHANGE": ""}] +819 4 \N 142856307 22 16285954 T TTTTATTTATA 565156 {22-16285954-TTATA-T,22-16285954-T-TTATA,22-16285954-T-TTTTATTTATA,22-16285954-TTA-T,22-16285954-T-TTATATATA,22-16285954-T-TTA} 4 0.0114547536 PASS 22-16285954-T-TTTTATTTATA 20 1746 {"DP": "39541", "FS": "0", "MQ": "58.41", "QD": "19.22", "VQSLOD": "-0.7886", "MQRankSum": "1.27", "BaseQRankSum": "-0.134", "ReadPosRankSum": "-0.653", "ClippingRankSum": "-0.036"} [{"LoF": "", "TSL": "", "CCDS": 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"EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "ENST00000343518.6:c.632+1276C>T", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "1/10", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", 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"SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant&NMD_transcript_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs201240366", "MOTIF_SCORE_CHANGE": ""}] +841 4 \N 76773885 22 16285997 G A 378445 {22-16285997-G-A} 280 0.434650451 VQSRTrancheSNP99.00to99.90 22-16285997-G-A 858 1974 {"DP": "39410", "FS": "0.541", "MQ": "54.82", "QD": "13.95", "VQSLOD": "-1.548", "MQRankSum": "-0.976", "BaseQRankSum": "1.09", "ReadPosRankSum": "-0.117", "ClippingRankSum": "-0.131"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": 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"ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs76773885", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "ENST00000343518.6:c.632+1257C>T", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "1/10", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs76773885", "MOTIF_SCORE_CHANGE": ""}] +844 4 \N 200465406 22 16286093 T A 7667.58008 {22-16286093-T-A} 2 0.0190190189 VQSRTrancheSNP99.00to99.90 22-16286093-T-A 38 1998 {"DP": "44575", "FS": "6.412", "MQ": "40.37", "QD": "3.95", "VQSLOD": "-19.32", "MQRankSum": "-1.444", "BaseQRankSum": "2.01", "ReadPosRankSum": "0.429", "ClippingRankSum": "-0.07", "InbreedingCoeff": "0.0342"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "ENST00000452800.1:c.464+1161A>T", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "A", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "1/11", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant&NMD_transcript_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", 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"POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs200465406", "MOTIF_SCORE_CHANGE": ""}] +846 4 \N 373761278 22 16286143 A G 32604.3008 {22-16286143-A-G} 12 0.105105102 VQSRTrancheSNP99.90to100.00 22-16286143-A-G 210 1998 {"DP": "46184", "FS": "44.075", "MQ": "37.07", "QD": "3.48", "VQSLOD": "-32.18", "MQRankSum": "0.137", "BaseQRankSum": "-1.635", "ReadPosRankSum": "0.272", "ClippingRankSum": "-0.116"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": 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"HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs373761278", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "ENST00000452800.1:c.464+1111T>C", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "G", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "1/11", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", 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"GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "intron_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs62224836", "MOTIF_SCORE_CHANGE": ""}] +851 4 \N 201077540 22 16286239 A G 391206 {22-16286239-A-G} 304 0.487987995 VQSRTrancheSNP99.90to100.00 22-16286239-A-G 975 1998 {"DP": "43446", "FS": "19.445", "MQ": "36.03", "QD": "11.26", "VQSLOD": "-26.92", "MQRankSum": "-1.85", "BaseQRankSum": "-0.39", "ReadPosRankSum": "0.196", "ClippingRankSum": "-0.12", "InbreedingCoeff": "-0.368"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": 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22-16286442-C-G 180 1948 {"DP": "28942", "FS": "4.609", "MQ": "55.42", "QD": "12.39", "VQSLOD": "-2.034", "MQRankSum": "-0.03", "BaseQRankSum": "2.54", "ReadPosRankSum": "0.212", "ClippingRankSum": "0.132"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "ENST00000452800.1:c.464+812G>C", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "G", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "1/11", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", 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"APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "593", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +974 4 \N \N 22 16288530 C CGTGCGCGCGCGGCGT 333083 {22-16288530-C-CGTGCGCGCGCGGCGT,22-16288530-C-CGTGCGCGCGGCGT,22-16288530-C-CGT,22-16288530-C-*} 0 0.175879404 PASS 22-16288530-C-CGTGCGCGCGCGGCGT 350 1990 {"DP": "70851", "FS": "9.997", "MQ": "55.47", "QD": "9.58", "VQSLOD": "-1.477", "MQRankSum": "-2.021", "BaseQRankSum": "-1.826", "ReadPosRankSum": "-0.305", "ClippingRankSum": "-0.027"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GTGCGCGCGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "813", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GTGCGCGCGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "593", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +975 4 \N \N 22 16288530 C CGTGCGCGCGGCGT 333083 {22-16288530-C-CGTGCGCGCGCGGCGT,22-16288530-C-CGTGCGCGCGGCGT,22-16288530-C-CGT,22-16288530-C-*} 0 0.123618089 PASS 22-16288530-C-CGTGCGCGCGGCGT 246 1990 {"DP": "70851", "FS": "9.997", "MQ": "55.47", "QD": "9.58", "VQSLOD": "-1.477", "MQRankSum": "-2.021", "BaseQRankSum": "-1.826", "ReadPosRankSum": "-0.305", "ClippingRankSum": "-0.027"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GTGCGCGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "813", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "2", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GTGCGCGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "593", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "2", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +976 4 \N \N 22 16288530 C CGT 333083 {22-16288530-C-CGTGCGCGCGCGGCGT,22-16288530-C-CGTGCGCGCGGCGT,22-16288530-C-CGT,22-16288530-C-*} 0 0.0190954767 PASS 22-16288530-C-CGT 38 1990 {"DP": "70851", "FS": "9.997", "MQ": "55.47", "QD": "9.58", "VQSLOD": "-1.477", "MQRankSum": "-2.021", "BaseQRankSum": "-1.826", "ReadPosRankSum": "-0.305", "ClippingRankSum": "-0.027"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "813", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "3", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "593", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "3", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +977 4 \N \N 22 16288530 C * 333083 {22-16288530-C-CGTGCGCGCGCGGCGT,22-16288530-C-CGTGCGCGCGGCGT,22-16288530-C-CGT,22-16288530-C-*} 0 0.0145728644 PASS 22-16288530-C-* 29 1990 {"DP": "70851", "FS": "9.997", "MQ": "55.47", "QD": "9.58", "VQSLOD": "-1.477", "MQRankSum": "-2.021", "BaseQRankSum": "-1.826", "ReadPosRankSum": "-0.305", "ClippingRankSum": "-0.027"} [] +978 4 \N 62224839 22 16288531 A G 412064 {22-16288531-A-G,22-16288531-A-ATGCGCGCGGCGTG,22-16288531-A-*} 0 0.328643203 PASS 22-16288531-A-G 654 1990 {"DP": "68638", "FS": "14.481", "MQ": "55.35", "QD": "11.64", "VQSLOD": "-0.3503", "MQRankSum": "-2.241", "BaseQRankSum": "0.491", "ReadPosRankSum": "-0.092", "ClippingRankSum": "0.01"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "G", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "594", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs62224839", 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"ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs62224839", "MOTIF_SCORE_CHANGE": ""}] +980 4 \N 62224839 22 16288531 A * 412064 {22-16288531-A-G,22-16288531-A-ATGCGCGCGGCGTG,22-16288531-A-*} 0 0.0140703516 PASS 22-16288531-A-* 28 1990 {"DP": "68638", "FS": "14.481", "MQ": "55.35", "QD": "11.64", "VQSLOD": "-0.3503", "MQRankSum": "-2.241", "BaseQRankSum": "0.491", "ReadPosRankSum": "-0.092", "ClippingRankSum": "0.01"} [] +981 4 \N \N 22 16288532 C T 9072.82031 {22-16288532-C-T,22-16288532-C-CGCGCG,22-16288532-C-*} 0 0.0115577886 VQSRTrancheINDEL99.00to99.90 22-16288532-C-T 23 1990 {"DP": "83726", "FS": "5.173", "MQ": "56.11", "QD": "4.48", "VQSLOD": "-2.348", "MQRankSum": "-0.227", "BaseQRankSum": "2.07", "ReadPosRankSum": "-0.952", "ClippingRankSum": 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"MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +983 4 \N \N 22 16288532 C * 9072.82031 {22-16288532-C-T,22-16288532-C-CGCGCG,22-16288532-C-*} 0 0.0140703516 VQSRTrancheINDEL99.00to99.90 22-16288532-C-* 28 1990 {"DP": "83726", "FS": "5.173", "MQ": "56.11", "QD": "4.48", "VQSLOD": "-2.348", "MQRankSum": "-0.227", "BaseQRankSum": "2.07", "ReadPosRankSum": "-0.952", "ClippingRankSum": "0.07"} [] +984 4 \N \N 22 16288536 T C 339934 {22-16288536-T-C,22-16288536-T-*} 2 0.32580322 VQSRTrancheSNP99.00to99.90 22-16288536-T-C 649 1992 {"DP": "66146", "FS": "18.181", "MQ": "55.12", "QD": "10.27", "VQSLOD": "-9.52", "MQRankSum": "-2.014", "BaseQRankSum": "-1.524", "ReadPosRankSum": "0.034", "ClippingRankSum": "0"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "C", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "819", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": 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"-9.972", "MQRankSum": "0.904", "BaseQRankSum": "0.666", "ReadPosRankSum": "0.339", "ClippingRankSum": "0.024"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "T", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "862", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": 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"ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "SNV", "cDNA_position": "", "Protein_position": "", "Existing_variation": "rs76076545", "MOTIF_SCORE_CHANGE": ""}] +999 4 \N \N 22 16288594 CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT C 65860.7031 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"HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1000 4 \N \N 22 16288594 CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT C 65860.7031 {22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGT-C,22-16288594-C-T,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C} 0 0.0125502013 VQSRTrancheINDEL99.00to99.90 22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C 25 1992 {"DP": "47015", "FS": "1.465", "MQ": "54.02", "QD": "11.37", "VQSLOD": "-1.828", "MQRankSum": "0.474", "BaseQRankSum": "0.529", "ReadPosRankSum": "-0.742", "ClippingRankSum": "0.041"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": 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"SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "CGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "657", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "2", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", 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"BaseQRankSum": "0.529", "ReadPosRankSum": "-0.742", "ClippingRankSum": "0.041"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "877", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "3", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "657", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "3", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1002 4 \N \N 22 16288594 CGCGCGTGCGGCGT C 65860.7031 {22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGT-C,22-16288594-C-T,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C} 20 0.0582329333 VQSRTrancheINDEL99.00to99.90 22-16288594-CGCGCGTGCGGCGT-C 116 1992 {"DP": "47015", "FS": "1.465", "MQ": "54.02", "QD": "11.37", "VQSLOD": "-1.828", "MQRankSum": "0.474", "BaseQRankSum": "0.529", "ReadPosRankSum": "-0.742", "ClippingRankSum": "0.041"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "877", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "4", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "657", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "4", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1003 4 \N \N 22 16288594 C T 65860.7031 {22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGT-C,22-16288594-C-T,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C} 0 0.0376506038 VQSRTrancheINDEL99.00to99.90 22-16288594-C-T 75 1992 {"DP": "47015", "FS": "1.465", "MQ": "54.02", "QD": "11.37", "VQSLOD": "-1.828", "MQRankSum": "0.474", "BaseQRankSum": "0.529", "ReadPosRankSum": "-0.742", "ClippingRankSum": "0.041"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "TGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "877", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "5", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "TGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "657", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "5", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1004 4 \N \N 22 16288594 CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT C 65860.7031 {22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGT-C,22-16288594-CGCGCGTGCGGCGT-C,22-16288594-C-T,22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C} 8 0.0391566269 VQSRTrancheINDEL99.00to99.90 22-16288594-CGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGT-C 78 1992 {"DP": "47015", "FS": "1.465", "MQ": "54.02", "QD": "11.37", "VQSLOD": "-1.828", "MQRankSum": "0.474", "BaseQRankSum": "0.529", "ReadPosRankSum": "-0.742", "ClippingRankSum": "0.041"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "CGCGCGTGCGGCGTGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "877", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "6", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "CGCGCGTGCGGCGTGCGCGTGCGGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "657", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "6", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "indel", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1008 4 \N \N 22 16288613 TGCGGC * 42498.6992 {22-16288613-TG-T,22-16288613-TGCGGC-*,22-16288613-TGCGGC-T} 40 0.133133128 VQSRTrancheINDEL99.00to99.90 22-16288613-TGCGGC-* 266 1998 {"DP": "49196", "FS": "1.393", "MQ": "54.21", "QD": "14.5", "VQSLOD": "-2.045", "MQRankSum": "2.12", "BaseQRankSum": "0.323", "ReadPosRankSum": "-1.374", "ClippingRankSum": "0.462"} [] +1011 4 \N \N 22 16288615 CGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTG * 42264.8008 {22-16288615-CGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTG-C,22-16288615-CGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTG-*} 40 0.133633628 VQSRTrancheINDEL99.00to99.90 22-16288615-CGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTG-* 267 1998 {"DP": "48686", "FS": "2.191", "MQ": "54.53", "QD": "14.14", "VQSLOD": "-2.263", "MQRankSum": "2.2", "BaseQRankSum": "0.304", "ReadPosRankSum": "-1.226", "ClippingRankSum": "0.784"} [] +1012 4 \N \N 22 16288616 GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC * 42446.6992 {22-16288616-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-*,22-16288616-G-A} 40 0.136136129 VQSRTrancheINDEL99.00to99.90 22-16288616-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-* 272 1998 {"DP": "48468", "FS": "1.389", "MQ": "53.68", "QD": "14.09", "VQSLOD": "-6.747", "MQRankSum": "-0.289", "BaseQRankSum": "1.3", "ReadPosRankSum": "1.17", "ClippingRankSum": "0", "InbreedingCoeff": "-60.1242"} [] +1014 4 \N \N 22 16288620 TGC T 40635.3984 {22-16288620-TGC-T,22-16288620-TGCGCGTGCGGCGTGCGCGTGC-*,22-16288620-TGCGCGTGCGGCGTGCGCGTGC-T} 2 0.0220220219 PASS 22-16288620-TGC-T 44 1998 {"DP": "46579", "FS": "1.616", "MQ": "53.4", "QD": "11.45", "VQSLOD": "-1.099", "MQRankSum": "1.07", "BaseQRankSum": "-0.052", "ReadPosRankSum": "-0.514", "ClippingRankSum": "-0.193", "InbreedingCoeff": "0.0218"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GCGTGCGGCGTGCGCGTGC", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "904", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GCGTGCGGCGTGCGCGTGC", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "684", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1015 4 \N \N 22 16288620 TGCGCGTGCGGCGTGCGCGTGC * 40635.3984 {22-16288620-TGC-T,22-16288620-TGCGCGTGCGGCGTGCGCGTGC-*,22-16288620-TGCGCGTGCGGCGTGCGCGTGC-T} 40 0.118618615 PASS 22-16288620-TGCGCGTGCGGCGTGCGCGTGC-* 237 1998 {"DP": "46579", "FS": "1.616", "MQ": "53.4", "QD": "11.45", "VQSLOD": "-1.099", "MQRankSum": "1.07", "BaseQRankSum": "-0.052", "ReadPosRankSum": "-0.514", "ClippingRankSum": "-0.193", "InbreedingCoeff": "0.0218"} [] +1018 4 \N \N 22 16288622 CGCGT C 36864 {22-16288622-CGCGTGCG-C,22-16288622-CGCGT-C,22-16288622-CGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGT-*} 0 0.0120120123 PASS 22-16288622-CGCGT-C 24 1998 {"DP": "48028", "FS": "1.528", "MQ": "53.57", "QD": "9.98", "VQSLOD": "-1.518", "MQRankSum": "0.536", "BaseQRankSum": "0.361", "ReadPosRankSum": "0.704", "ClippingRankSum": "0.347"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "906", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "2", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "GCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGT", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "686", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "2", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1019 4 \N \N 22 16288622 CGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGT * 36864 {22-16288622-CGCGTGCG-C,22-16288622-CGCGT-C,22-16288622-CGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGT-*} 22 0.091091089 PASS 22-16288622-CGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGT-* 182 1998 {"DP": "48028", "FS": "1.528", "MQ": "53.57", "QD": "9.98", "VQSLOD": "-1.518", "MQRankSum": "0.536", "BaseQRankSum": "0.361", "ReadPosRankSum": "0.704", "ClippingRankSum": "0.347"} [] +1022 4 \N \N 22 16288626 TGCGGC T 35343.3984 {22-16288626-TGCGGC-T,22-16288626-TGCGGC-*} 2 0.0220220219 VQSRTrancheINDEL99.00to99.90 22-16288626-TGCGGC-T 44 1998 {"DP": "47421", "FS": "0.742", "MQ": "53.32", "QD": "10.17", "VQSLOD": "-2.222", "MQRankSum": "1.09", "BaseQRankSum": "0.332", "ReadPosRankSum": "-0.903", "ClippingRankSum": "-0.173", "InbreedingCoeff": "-2.0711"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "690", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "910", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1023 4 \N \N 22 16288626 TGCGGC * 35343.3984 {22-16288626-TGCGGC-T,22-16288626-TGCGGC-*} 22 0.0810810775 VQSRTrancheINDEL99.00to99.90 22-16288626-TGCGGC-* 162 1998 {"DP": "47421", "FS": "0.742", "MQ": "53.32", "QD": "10.17", "VQSLOD": "-2.222", "MQRankSum": "1.09", "BaseQRankSum": "0.332", "ReadPosRankSum": "-0.903", "ClippingRankSum": "-0.173", "InbreedingCoeff": "-2.0711"} [] +1025 4 \N \N 22 16288628 CG * 29620.0996 {22-16288628-CG-C,22-16288628-CG-*} 22 0.0920920894 VQSRTrancheINDEL99.00to99.90 22-16288628-CG-* 184 1998 {"DP": "46493", "FS": "0.786", "MQ": "52.32", "QD": "10.03", "VQSLOD": "-1.861", "MQRankSum": "1.32", "BaseQRankSum": "0.478", "ReadPosRankSum": "-1.369", "ClippingRankSum": "0.437"} [] +1026 4 \N \N 22 16288629 GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC G 31046.3008 {22-16288629-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-G,22-16288629-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-*} 2 0.0175175183 VQSRTrancheINDEL99.00to99.90 22-16288629-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-G 35 1998 {"DP": "46349", "FS": "0", "MQ": "52.66", "QD": "8.09", "VQSLOD": "-2.532", "MQRankSum": "0.143", "BaseQRankSum": "0.4", "ReadPosRankSum": "-0.784", "ClippingRankSum": "-0.203"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "693", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}, {"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "913", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1027 4 \N \N 22 16288629 GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC * 31046.3008 {22-16288629-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-G,22-16288629-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-*} 22 0.0905905887 VQSRTrancheINDEL99.00to99.90 22-16288629-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-* 181 1998 {"DP": "46349", "FS": "0", "MQ": "52.66", "QD": "8.09", "VQSLOD": "-2.532", "MQRankSum": "0.143", "BaseQRankSum": "0.4", "ReadPosRankSum": "-0.784", "ClippingRankSum": "-0.203"} [] +1028 4 \N \N 22 16288630 G * 30090.6992 {22-16288630-G-*,22-16288630-G-A} 22 0.102602601 VQSRTrancheSNP99.00to99.90 22-16288630-G-* 205 1998 {"DP": "46712", "FS": "0", "MQ": "49.49", "QD": "8.1", "VQSLOD": "-6.98", "MQRankSum": "-1.316", "BaseQRankSum": "-0.57", "ReadPosRankSum": "1.67", "ClippingRankSum": "0.137"} [] +1030 4 \N \N 22 16288631 CGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGG * 30129.5996 {22-16288631-CGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGG-*,22-16288631-CGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGG-C} 22 0.1011011 PASS 22-16288631-CGTGCGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCGG-* 202 1998 {"DP": "46046", "FS": "0", "MQ": "51.34", "QD": "8.26", "VQSLOD": "-1.485", "MQRankSum": "-1.772", "BaseQRankSum": "1.92", "ReadPosRankSum": "-0.083", "ClippingRankSum": "0.77"} [] +1033 4 \N \N 22 16288633 TGC * 27163.9004 {22-16288633-TGC-T,22-16288633-TGC-*} 22 0.0800800771 PASS 22-16288633-TGC-* 160 1998 {"DP": "46751", "FS": "0.769", "MQ": "52.86", "QD": "9.45", "VQSLOD": "-1.574", "MQRankSum": "0.1", "BaseQRankSum": "1.3", "ReadPosRankSum": "0.556", "ClippingRankSum": "0.06"} [] +1034 4 \N \N 22 16288635 CGCGTGCG * 16258.0996 {22-16288635-CGCGTGCG-*,22-16288635-C-CGCGTGCGGCGTGCGCGTGCG,22-16288635-CGCGTGCG-C} 8 0.0520520508 PASS 22-16288635-CGCGTGCG-* 104 1998 {"DP": "46528", "FS": "0", "MQ": "52.78", "QD": "6.86", "VQSLOD": "-1.44", "MQRankSum": "-0.648", "BaseQRankSum": "0.375", "ReadPosRankSum": "-0.785", "ClippingRankSum": "0.05"} [] +1041 4 \N \N 22 16288655 GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC * 10232 {22-16288655-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-*,22-16288655-GGCGTGC-G} 6 0.0355355367 VQSRTrancheINDEL99.00to99.90 22-16288655-GGCGTGCGCGTGCGGCGTGCGCGTGCGGCGTGC-* 71 1998 {"DP": "45064", "FS": "1.921", "MQ": "54.97", "QD": "5.35", "VQSLOD": "-2.176", "MQRankSum": "-1.48", "BaseQRankSum": "0.659", "ReadPosRankSum": "-1.283", "ClippingRankSum": "1.31"} [] +1044 4 \N \N 22 16288661 CGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCG * 5375.31006 {22-16288661-CGCGTGCGGCGTGCGCGTGCG-C,22-16288661-CGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCG-*} 0 0.0220661983 PASS 22-16288661-CGCGTGCGGCGTGCGCGTGCGGCGTGCGCGTGCG-* 44 1994 {"DP": "44069", "FS": "3.428", "MQ": "51.88", "QD": "3.16", "VQSLOD": "-1.271", "MQRankSum": "-0.967", "BaseQRankSum": "-0.731", "ReadPosRankSum": "-0.096", "ClippingRankSum": "0.391", "InbreedingCoeff": "0.0093"} [] +1046 4 \N \N 22 16288668 GGCGTGCGCGTGCGGCGTGC * 4362.47021 {22-16288668-GGCGTGCGCGTGCGGCGTGC-G,22-16288668-GGCGTGCGCGTGCGGCGTGC-*} 0 0.0220661983 VQSRTrancheINDEL99.00to99.90 22-16288668-GGCGTGCGCGTGCGGCGTGC-* 44 1994 {"DP": "43432", "FS": "4.033", "MQ": "52.53", "QD": "2.44", "VQSLOD": "-1.802", "MQRankSum": "-1.592", "BaseQRankSum": "0.776", "ReadPosRankSum": "0.694", "ClippingRankSum": "1.16"} [] +1047 4 \N \N 22 16288681 GGCGTGC G 5723.83984 {22-16288681-GGCGTGC-G,22-16288681-GGCGTGC-*} 0 0.01252505 PASS 22-16288681-GGCGTGC-G 25 1996 {"DP": "43625", "FS": "7.181", "MQ": "50.14", "QD": "2.37", "VQSLOD": "-1.558", "MQRankSum": "-0.384", "BaseQRankSum": "0.478", "ReadPosRankSum": "0.324", "ClippingRankSum": "-0.342"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "-", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "965", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "", "ALLELE_NUM": "1", "GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": 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"", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1048 4 \N \N 22 16288681 GGCGTGC * 5723.83984 {22-16288681-GGCGTGC-G,22-16288681-GGCGTGC-*} 0 0.0240480956 PASS 22-16288681-GGCGTGC-* 48 1996 {"DP": "43625", "FS": "7.181", "MQ": "50.14", "QD": "2.37", "VQSLOD": "-1.558", "MQRankSum": "-0.384", "BaseQRankSum": "0.478", "ReadPosRankSum": "0.324", "ClippingRankSum": "-0.342"} [] +1050 4 \N \N 22 16288684 G * 4864.02002 {22-16288684-G-C,22-16288684-G-*} 0 0.0315631256 VQSRTrancheSNP99.00to99.90 22-16288684-G-* 63 1996 {"DP": "43562", "FS": "3.626", "MQ": 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16288739 T G 495277 {22-16288739-T-G} 340 0.466244727 VQSRTrancheSNP99.00to99.90 22-16288739-T-G 884 1896 {"DP": "36880", "FS": "3.258", "MQ": "52.91", "QD": "19.5", "VQSLOD": "-3.051", "MQRankSum": "-1.751", "BaseQRankSum": "0.021", "ReadPosRankSum": "0.463", "ClippingRankSum": "-0.038", "InbreedingCoeff": "-0.294"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "G:0.4391", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "cds_start_NF", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "G", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "H0YG78_HUMAN", "AFR_MAF": "G:0.5711", "AMR_MAF": "G:0.4481", "BIOTYPE": "nonsense_mediated_decay", "DOMAINS": "", "EAS_MAF": "G:0.2163", "EUR_MAF": "G:0.4751", "Feature": "ENST00000452800", "HGNC_ID": "133", "SAS_MAF": "G:0.4468", "SOMATIC": "", "UNIPARC": "UPI000204A808", "CLIN_SIG": "", "DISTANCE": "1022", 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16288742 G C 1005040 {22-16288742-G-C} 844 0.702105284 VQSRTrancheSNP99.00to99.90 22-16288742-G-C 1334 1900 {"DP": "35702", "FS": "2.885", "MQ": "53.32", "QD": "30.51", "VQSLOD": "-3.356", "MQRankSum": "-2.757", "BaseQRankSum": "-0.389", "ReadPosRankSum": "0.231", "ClippingRankSum": "-0.06", "InbreedingCoeff": "-0.287"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "G:0.2065", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "C", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "C:0.8964", "AMR_MAF": "C:0.7695", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "C:0.6776", "EUR_MAF": "C:0.7803", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "C:0.8047", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "805", "ExAC_MAF": "", 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376342664 22 16288764 T C 37932.8008 {22-16288764-T-C} 18 0.134036139 VQSRTrancheSNP99.00to99.90 22-16288764-T-C 267 1992 {"DP": "40244", "FS": "11.702", "MQ": "52.51", "QD": "4.34", "VQSLOD": "-5.369", "MQRankSum": "-1.876", "BaseQRankSum": "0.594", "ReadPosRankSum": "-0.747", "ClippingRankSum": "-0.057", "InbreedingCoeff": "-0.1182"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "C", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "827", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", 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0.273000002 VQSRTrancheSNP99.90to100.00 22-16291904-G-C 546 2000 {"DP": "41382", "FS": "97.468", "MQ": "39.19", "QD": "5.2", "VQSLOD": "-49.57", "MQRankSum": "-0.841", "BaseQRankSum": "-2.896", "ReadPosRankSum": "1.22", "ClippingRankSum": "0"} [{"LoF": "", "TSL": "", "CCDS": "CCDS46658.1", "ENSP": "ENSP00000340610", "EXON": "", "GMAF": "", "Gene": "ENSG00000198062", "SIFT": "", "FLAGS": "", "HGVSc": "", "HGVSp": "", "PHENO": "", "AA_MAF": "", "APPRIS": "", "Allele": "C", "Codons": "", "EA_MAF": "", "IMPACT": "MODIFIER", "INTRON": "", "PUBMED": "", "STRAND": "-1", "SYMBOL": "POTEH", "TREMBL": "", "AFR_MAF": "", "AMR_MAF": "", "BIOTYPE": "protein_coding", "DOMAINS": "", "EAS_MAF": "", "EUR_MAF": "", "Feature": "ENST00000343518", "HGNC_ID": "133", "SAS_MAF": "", "SOMATIC": "", "UNIPARC": "UPI0000E5A425", "CLIN_SIG": "", "DISTANCE": "3967", "ExAC_MAF": "", "LoF_info": "", "PolyPhen": "", "CANONICAL": "YES", "LoF_flags": "", "MOTIF_POS": "", "SWISSPROT": "POTEH_HUMAN", "ALLELE_NUM": "1", 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"Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1211 4 \N \N 22 16292001 CGT C 80846.1016 {22-16292001-CGT-C,22-16292001-C-T,22-16292001-C-CGTGTGT,22-16292001-C-CGTGT,22-16292001-C-CGT,22-16292001-CGTGTGTGTGT-*} 8 0.11133603 VQSRTrancheINDEL99.00to99.90 22-16292001-CGT-C 220 1976 {"DP": "48022", "FS": "0.861", "MQ": "46.35", "QD": "3.85", "VQSLOD": "-1.998", "MQRankSum": "-2.243", "BaseQRankSum": "0.553", "ReadPosRankSum": "-0.168", "ClippingRankSum": "-0.06"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", "GMAF": "", "Gene": 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"LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1212 4 \N \N 22 16292001 C T 80846.1016 {22-16292001-CGT-C,22-16292001-C-T,22-16292001-C-CGTGTGT,22-16292001-C-CGTGT,22-16292001-C-CGT,22-16292001-CGTGTGTGTGT-*} 0 0.0146761136 VQSRTrancheINDEL99.00to99.90 22-16292001-C-T 29 1976 {"DP": "48022", "FS": "0.861", "MQ": "46.35", "QD": "3.85", "VQSLOD": "-1.998", "MQRankSum": "-2.243", "BaseQRankSum": "0.553", "ReadPosRankSum": "-0.168", "ClippingRankSum": "-0.06"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": "ENSP00000442107", "EXON": "", 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"GENE_PHENO": "", "LoF_filter": "", "MOTIF_NAME": "", "Amino_acids": "", "Consequence": "upstream_gene_variant", "HGVS_OFFSET": "", "CDS_position": "", "ExAC_AFR_MAF": "", "ExAC_AMR_MAF": "", "ExAC_Adj_MAF": "", "ExAC_EAS_MAF": "", "ExAC_FIN_MAF": "", "ExAC_NFE_MAF": "", "ExAC_OTH_MAF": "", "ExAC_SAS_MAF": "", "Feature_type": "Transcript", "HIGH_INF_POS": "", "SYMBOL_SOURCE": "HGNC", "VARIANT_CLASS": "sequence_alteration", "cDNA_position": "", "Protein_position": "", "Existing_variation": "", "MOTIF_SCORE_CHANGE": ""}] +1214 4 \N \N 22 16292001 C CGTGT 80846.1016 {22-16292001-CGT-C,22-16292001-C-T,22-16292001-C-CGTGTGT,22-16292001-C-CGTGT,22-16292001-C-CGT,22-16292001-CGTGTGTGTGT-*} 0 0.017206477 VQSRTrancheINDEL99.00to99.90 22-16292001-C-CGTGT 34 1976 {"DP": "48022", "FS": "0.861", "MQ": "46.35", "QD": "3.85", "VQSLOD": "-1.998", "MQRankSum": "-2.243", "BaseQRankSum": "0.553", "ReadPosRankSum": "-0.168", "ClippingRankSum": "-0.06"} [{"LoF": "", "TSL": "", "CCDS": "", "ENSP": 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--- a/test/travis_script.sh +++ b/test/travis_script.sh @@ -28,13 +28,14 @@ echo '>>> Test 2. Load the swefreq schema' psql -U postgres -h 127.0.0.1 -p 5433 -f sql/data_schema.sql psql -U postgres -h 127.0.0.1 -p 5433 -f sql/user_schema.sql psql -U postgres -h 127.0.0.1 -p 5433 -f test/data/load_dummy_data.sql +psql -U postgres -h 127.0.0.1 -p 5433 -f test/data/browser_test_data.sql echo '>>> Test 3. Check that the backend starts' (cd backend && ../test/01_daemon_starts.sh) echo '>>> Test 4. the backend API' -coverage run backend/route.py --port=4000 --develop 1>http_log.txt 2>&1 & +COVERAGE_FILE=.coverage_server coverage run backend/route.py --port=4000 --develop 1>http_log.txt 2>&1 & BACKEND_PID=$! sleep 2 # Lets wait a little bit so the server has started @@ -59,10 +60,16 @@ RETURN_VALUE=0 python backend/test.py -v RETURN_VALUE=$((RETURN_VALUE + $?)) +# test browser +COVERAGE_FILE=.coverage_pytest PYTHONPATH=$PYTHONPATH:backend/ py.test backend/ --cov=backend/ +RETURN_VALUE=$((RETURN_VALUE + $?)) + # Quit the app curl localhost:4000/developer/quit sleep 2 # Lets wait a little bit so the server has stopped +coverage combine .coverage_pytest .coverage_server + if [ -f .coverage ]; then coveralls coverage report