@holtgrewe holtgrewe released this Apr 26, 2018 · 44 commits to master since this release

Assets 2

As in all recent releases, Jannovar is best installed through Maven Central.

overall

  • Changing HTSJDK version to 2.14.3
  • Using the one letter amino acid code in HGVS representation as default (changes in core, hgvs, htsjdk and cli). Now the cli option --3-letter-amino-acids works as expected.

jannovar-cli

jannovar-vardbs

  • Replacing whitespace with string when annotating from TSV file.

jannovar-htsjdk

  • Fixing bug in GenomeRegionSequenceExtraction. Error reports always sequences from the first contig in the referebnce file and not the requested contig. Affects only the cli command hgvs-to-vcf.

@visze visze released this Jan 16, 2018 · 75 commits to master since this release

Assets 2

overall

  • Changing HTSJDK version to 2.14.0
  • Codestyle approvements

jannovar-cli

  • Fixing annotation with Polyphen prediction (data type)

jannovar-core

  • Fixing mendelian "bug" #393 (has no affect because check was not necessary)
  • New inheritance mode: mitochondrial
  • Bugfix ProgressBar (doPrint was always true)

jannovar-vardbs

  • Fixed problem with interpretation of Clinvar annotation origin.
  • Clinvar BEST_AC and BEST_AF are now named AC_POPMAX and AF_POPMAX to be consitent with gnomAD

@holtgrewe holtgrewe released this Aug 29, 2017 · 138 commits to master since this release

Assets 2

overall

  • Changing Guava version to 0.22
  • Changing slf4j version to 1.7.24
  • Changing log4j version to 2.8.2

jannovar-cli

  • Adding experimental support for annotating with VCF files.
  • Adding experimental support for annotating with tabix-indexed TSV files and dbNSFP.
  • Integrating the advanced pedigree-based filters (useful for filtration to de novo variants).
  • Making it possible to override database INI settings using user-specified INI files.

jannovar-core

  • Fixing stop loss annotation (#351).
  • Finishing renaming of TranscriptInfo to TranscriptModel (#348).
  • Upstream and downstream variant were considered "not off exome". They now are.

jannovar-filter

  • Adding code for performing more advanced filtration/annotation filtering to de novo variants.
  • Improving documentation of MaxFreqAr and MaxFreqAd in header.

jannovar-vardbs

  • Adding experimental support for annotating with VCF files
  • Adding experimental support for annotating with tabix-indexed TSV files and dbNSFP

jannovar-filter

  • Fixing bug that ignored variant filters for recessive annotation

@holtgrewe holtgrewe released this May 8, 2017 · 173 commits to master since this release

Assets 2

As in all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.22.jar.

jannovar-htsjdk

  • Fixin NPE problem with inheritance annotation

jannovar-statistics

  • Also counting number of variants on contigs
  • Fixing counting bug that made UTR3 variants be counted as UTR5
  • Fixing NPE in case of null variant annotations (e.g., unknown contig)

jannovar-vardbs

  • Fixing a problem with normalization on variant annotation
  • Fixing problem with default value of CLNSIG ("25" -> "255")

jannovar-filter

  • Incorporating gnomAD annotation into exclusion by frequency for inheritance filter (#343)
  • Fixing header description for MinAafHomAlt and MaxAafHomRef (#342)

jannovar-cli

  • Checking that reference is given also for gnomAD VCF annotation

@holtgrewe holtgrewe released this Apr 4, 2017 · 189 commits to master since this release

Assets 2

As in all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.21.jar.

all

  • Fixing language in mvn surfire plugin. Now mvn tests work on locale de_DE etc..

jannovar-cli

  • Adding --interval argument for only processing a part of the file
  • Adding statistics command for computing statistics on variants in VCF file
  • Fixing bug in HGVS to VCF
  • Better handling missing .dict file for HGVS to VCF translation
  • Adding --annotate-as-singleton-pedigree parameter for annotation of singleton pedigrees without pedigree file (single individual is assumed to be affected)
  • More friendly user message in case of unsorted files on inheritance mode annotation
  • Interpretation of filters in compatible inheritance mode annotation
  • Integrating new jannovar-filter into Jannovar CLI.
    Filtered genotypes will be passed into the inheritance filter as no-call.
  • Adding annotation with ClinVar
  • Printing warnings next to the annotations in annotate-pos
  • AR inheritance annotation of two siblings bugfix (no parents avaiable in comp.het mode) #314

jannovar-filter

  • Adding functionality to add filters based on frequencies found in dbSNP and ExAC
  • Adding back as module for threshold-based filtration.
    This module allows to create genotype-wise soft-filters for low coverage.
    Also, variants can be soft-filtered based on whether the genotype calls of all affected individuals are filtered out.

jannovar-core

  • Extending API to expose mendelian checks for comp het./ad alt (via SubModuleOfInheritance and MendelianInheritanceChecker
  • Jannovar version is now written out to database file which allows better error checks and compatibility messages
  • Un-deprecating BestAnnotationListTextGenerator and AllAnnotationListTextGenerator classes, useful for text-based output formats
  • Changing behaviour of VariantEffect.isOffExome() and adding a variant that allows to decide between UTR on/off exome and non-consensus splice region on/off exome
  • Making the behaviour of overriding transcripts configurable at least in the code, using default to not do this any more
  • Adding WARNING_REF_DOES_NOT_MATCH_TRANSCRIPT to AnnotationMessage
  • Properly pushing through warnings from the annotators into the returned VariantAnnotation object
  • Pedigree files are now more compatible to the PLINK format
    • whitespace separated instead of tab separated (read only, written as TSV)
    • interpreting any value not in {1, 2} to be "unknown" sex instead (coded as 0) of throwing

jannovar-htsjdk

  • Fixing bug in transcript-to-genome translation, in HGVS the stop codon is not part of the CDS but in TranscriptModel it is
  • Optional interpretation of certain filters in GeneWiseMendelianAnnotationProcessor.
  • Extending interface of VariantContextAnnotator for automatic error annotation generation, previously in jannovar-cli
  • Adding VariantEffectHeaderExtender class to jannovar-htsjdk
  • Fixing bug with problems of unmodifiable Attributes (error annotation).

jannovar-vardbs

  • Also writing out variant allele origin for dbSNP
  • Adding annotation with COSMIC
  • Fixing header description for exac database
  • Fixing output of DBSNP_CAF to also contain reference allele AF
  • Adding annotation with ClinVar, can annotate all clinvar variants

jannovar-inheritance-checker

  • Removing this outdated module.
    Use the classes in de.charite.compbio.jannovar.mendel instead

jannovar-stats

  • all-new module for gathering statistics on VCF files

@holtgrewe holtgrewe released this Dec 19, 2016 · 274 commits to master since this release

Assets 2

As in all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.20.jar.

all

  • Change email/organisations in master pom

jannovar-core

  • GenotypeCalls.getGenotypeForSample() returns a "no-call" genotype now instead of null

jannovar-htsjdk

  • fix to annotation with compatible mode of inheritance (#289)
  • update to htsjdk 2.8.1

jannovar-cli

  • removing requirement for proper contig contig lines in gene-wise gene annotation
  • fixing NPE in the case of no contig lines
  • improving error message on samples in VCF file that are not in pedigree
  • fix to annotation with compatible mode of inheritance (#289)
  • better overview on CLI help message
  • if ref-fasta is not set properly a nicer error message will be shown.

jannovar-vardbs

  • Fixing bug with problems of unmodifieable Attributes.
  • Including Hom/Het/Hemi counds of ExAC (#295)
  • update to htsjdk 2.8.1

@holtgrewe holtgrewe released this Dec 8, 2016 · 307 commits to master since this release

Assets 2

This is a bugfix release.

As with all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.19.jar.

manual

  • Manual loads version from central POM file now
  • Adjusting manual links to point to javadoc.io

jannovar-core

  • Fixing integration of HGNC into the downloaded databases
    • For UCSC, HGNC records are searched based on the Entrez ID.
      If HGNC does not know the Entrez then only the Entrez ID from UCSC is written as additional ID.
    • For RefSeq, linking is done through Entrez ID.
      If HGNC does not know the Entrez then only the Entrez ID from RefSeq is written as additional ID.
    • For ENSEMBL linking is done through the ENSEMBL gene id.
      If this is not known to HGNC then no additional IDs are annotated.
  • Fixing problem with UnsupportedOperationException in jannovar-htsjdk

@holtgrewe holtgrewe released this Dec 8, 2016 · 316 commits to master since this release

Assets 2

As with all recent releases, Jannovar is best installed through Maven Central.
Alternatively you can directly download the compiled jannovar-cli-0.18.jar.

all

  • replace charite email of p. robinson with the new one of jax

jannovar-cli

  • Renaming tx-to-chrom to hgvs-to-vcf, also in Java module names.
  • CLI changes such that one VCF input and one VCF output path can be used only
  • Replacing apache commons-cli with argparse4j for a more modern and usable CLI
  • Consistently writing out HUGO symbols for gene names, using the hgnc_complete_set.txt information downloaded when building the annotation DB
  • Upgrading from ENSEMBL-74 to ENSEMBL-75 for annotation database files
  • Removing support for old Jannovar-style annotations (#241)
  • Adding new command for annotating csv files (annotate-csv)

jannovar-htsjdk

  • Properly annotating Mendelian inheritance for intergenic variants

jannovar-core

  • downloading hgnc_complete_set.txt together with data sets, TranscriptModel objects now consistently contain additional IDs
  • making ENSEMBL parsing more robust (falling back to transcript name if no transcript ID)
  • fixing bug #248 for ENSEMBL that used gene_id for gene_name
  • bugfix of NullPointerException in RefSeqParser while parsing refSeq curated
  • bugfix space in SeqOID of SYNONYMOUS_VARIANT
  • Update link to HGVS Nomenclature
  • Now BestAnnotationListTextGenerator shows really the best and not all annotations!

Manual

  • Documenting cli changes
  • Adding additional sites contributing, FAQ and how to filter
  • Better description of installations and quickstart