/
mip_download_rd_dna_config_-1.0-.yaml
1051 lines (1051 loc) · 50.1 KB
/
mip_download_rd_dna_config_-1.0-.yaml
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---
bash_set_errexit: 1
bash_set_pipefail: 1
load_env:
mip_rd_dna:
method: conda
mip:
project_id: development
reference:
1000g_indels:
- phase1
1000g_omni:
- 2.5
1000g_sites:
- phase3_v4_20130502
1000g_snps:
- phase1
cadd_offline_annotations:
- v1.6
cadd_to_vcf_header:
- 1.0
cadd_whole_genome_snvs:
- v1.4
- v1.5
- v1.6
chromograph_cytoband:
- v1.0
clinvar:
- 20211010
- 20220829
dbnsfp:
- 3.5a
- 4.1a
- 4.3a
dbsnp:
- 138_esa_129
- 138
- gold_standard_dbsnp
- 146
delly_exclude:
- 20150915
- 20200310
expansionhunter:
- 4.0.2
- 5.0.0
gatk_mitochondrial_ref:
- v0_m_amb
- v0_m_ann
- v0_m_blacklist
- v0_m_blacklist_shifted
- v0_m_bwt
- v0_m_control_shifted_interval_list
- v0_m_dict
- v0_m_fasta
- v0_m_non_control_interval_list
- v0_m_numt_interval
- v0_m_pac
- v0_m_sa
- v0_m_shiftback
- v0_m_shifted_amb
- v0_m_shifted_ann
- v0_m_shifted_bwt
- v0_m_shifted_dict
- v0_m_shifted_fasta
- v0_m_shifted_pac
- v0_m_shifted_sa
genbank_haplogroup:
- 20150801
genomic_superdups:
- 20181009
- 20190826
giab:
- na12878_v2.19_bed
- na12878_v2.19_wgs
- na12878_v3.3.2_bed
- na12878_v3.3.2_wgs
- na12878_v4.2.1_bed
- na12878_v4.2.1_wgs
- na24143_v3.3.2_bed
- na24143_v3.3.2_wgs
- na24143_v4.2.1_bed
- na24143_v4.2.1_wgs
- na24385_v3.3.2_bed
- na24385_v3.3.2_wgs
- na24385_v4.2.1_bed
- na24385_v4.2.1_wgs
- na24631_v3.3.2_bed
- na24631_v3.3.2_wgs
- na24631_v4.2.1_bed
- na24631_v4.2.1_wgs
gnomad:
- r2.0.1
- r2.1.1
- r2.1.1_sv
gnomad_chrsplit:
- r3.1.1
- r3.1.2
gnomad_mt:
- r3.1
gnomad_pli_per_gene:
- r2.1.1
hapmap:
- 3.3
human_reference:
- decoy_5
- assembly38
- assembly38_alt
manta_call_regions:
- 1.0
mills_and_1000g_indels:
- gold_standard_indels
rank_model:
- v0.2
- v1.33
- v1.34
reduced_penetrance:
- 2017
scout_exons:
- 200917
- 201701
sv_vcfanno_config:
- v0.2
- v1.3
- v1.4
svrank_model:
- v0.1
- v1.8
- v1.9
vcf2cytosure_blacklist_regions:
- 1.0
- 200520
vcfanno_config:
- v0.2
- v1.17
- v1.18
vcfanno_functions:
- v1.0
reference_feature:
human_reference:
grch37:
decoy_5:
file: human_g1k_v37_decoy.fasta.gz
file_check: human_g1k_v37_decoy.fasta.gz.md5
outfile: grch37_homo_sapiens_-d5-.fasta.gz
outfile_check: grch37_homo_sapiens_-d5-.fasta.gz.md5
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
outfile_decompress: gzip
outfile_check_method: md5sum
grch38:
assembly38:
file: Homo_sapiens_assembly38.fasta
file_index: Homo_sapiens_assembly38.fasta.fai
outfile: grch38_homo_sapiens_-assembly-.fasta
outfile_index: grch38_homo_sapiens_-assembly-.fasta.fai
url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
assembly38_alt:
file: Homo_sapiens_assembly38.fasta.64.alt
outfile: grch38_homo_sapiens_-assembly-.fasta.alt
url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
1000g_indels:
grch37:
phase1:
file: 1000G_phase1.indels.b37.vcf.gz
file_check: 1000G_phase1.indels.b37.vcf.gz.md5
file_index: 1000G_phase1.indels.b37.vcf.idx.gz
file_index_check: 1000G_phase1.indels.b37.vcf.idx.gz.md5
outfile: grch37_1000g_indels_-phase1-.vcf.gz
outfile_check: grch37_1000g_indels_-phase1-.vcf.gz.md5
outfile_index: grch37_1000g_indels_-phase1-.vcf.idx.gz
outfile_index_check: grch37_1000g_indels_-phase1-.vcf.idx.gz.md5
outfile_decompress: gzip
outfile_index_decompress: gzip
outfile_check_method: md5sum
outfile_index_check_method: md5sum
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
grch38:
phase1:
file: Homo_sapiens_assembly38.known_indels.vcf.gz
file_index: Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
outfile: grch38_1000g_indels_-phase1-.vcf.gz
outfile_index: grch38_1000g_indels_-phase1-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
1000g_omni:
grch37:
2.5:
file: 1000G_omni2.5.b37.vcf.gz
file_check: 1000G_omni2.5.b37.vcf.gz.md5
file_index: 1000G_omni2.5.b37.vcf.idx.gz
file_index_check: 1000G_omni2.5.b37.vcf.idx.gz.md5
outfile: grch37_1000g_omni_-2.5-.vcf.gz
outfile_check: grch37_1000g_omni_-2.5-.vcf.gz.md5
outfile_index: grch37_1000g_omni_-2.5-.vcf.idx.gz
outfile_index_check: grch37_1000g_omni_-2.5-.vcf.idx.gz.md5
outfile_decompress: gzip
outfile_index_decompress: gzip
outfile_check_method: md5sum
outfile_index_check_method: md5sum
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
grch38:
2.5:
file: 1000G_omni2.5.hg38.vcf.gz
file_index: 1000G_omni2.5.hg38.vcf.gz.tbi
outfile: grch38_1000g_omni_-2.5-.vcf.gz
outfile_index: grch38_1000g_omni_-2.5-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
1000g_sites:
grch37:
phase3_v4_20130502:
file: 1000G_phase3_v4_20130502.sites.vcf.gz
file_index: 1000G_phase3_v4_20130502.sites.vcf.gz.tbi
outfile: grch37_1000g_sites_-phase3_v4_2013-05-02-.vcf.gz
outfile_index: grch37_1000g_sites_-phase3_v4_2013-05-02-.vcf.gz.tbi
outfile_decompress: gzip
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
1000g_snps:
grch37:
phase1:
file: 1000G_phase1.snps.high_confidence.b37.vcf.gz
file_check: 1000G_phase1.snps.high_confidence.b37.vcf.gz.md5
file_index: 1000G_phase1.snps.high_confidence.b37.vcf.idx.gz
file_index_check: 1000G_phase1.snps.high_confidence.b37.vcf.idx.gz.md5
outfile: grch37_1000g_snps_high_confidence_-phase1-.vcf.gz
outfile_check: grch37_1000g_snps_high_confidence_-phase1-.vcf.gz.md5
outfile_index: grch37_1000G_snps_high_confidence_-phase1-.vcf.idx.gz
outfile_index_check: grch37_1000G_snps_high_confidence_-phase1-.vcf.idx.gz.md5
outfile_decompress: gzip
outfile_index_decompress: gzip
outfile_check_method: md5sum
outfile_index_check_method: md5sum
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
grch38:
phase1:
file: 1000G_phase1.snps.high_confidence.hg38.vcf.gz
file_index: 1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
outfile: grch38_1000g_snps_high_confidence_-phase1-.vcf.gz
outfile_index: grch38_1000g_snps_high_confidence_-phase1-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/
cadd_offline_annotations:
grch37:
v1.6:
file: annotationsGRCh37_v1.6.tar.gz
file_check: annotationsGRCh37_v1.6.tar.gz.md5
outfile: annotationsGRCh37_v1.6.tar.gz
outfile_check: annotationsGRCh37_v1.6.tar.gz.md5
outfile_check_method: md5sum
outfile_decompress: tar
url_prefix: https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh37/
grch38:
v1.6:
file: annotationsGRCh38_v1.6.tar.gz
file_check: annotationsGRCh38_v1.6.tar.gz.md5
outfile: annotationsGRCh38_v1.6.tar.gz
outfile_check: annotationsGRCh38_v1.6.tar.gz.md5
outfile_check_method: md5sum
outfile_decompress: tar
url_prefix: https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh38/
cadd_to_vcf_header:
grch37:
1.0:
file: grch37_cadd_to_vcf_header_-1.0-.txt
file_check: grch37_cadd_to_vcf_header_-1.0-.txt.md5
outfile: cadd_to_vcf_header_-1.0-.txt
outfile_check: cadd_to_vcf_header_-1.0-.txt.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
cadd_whole_genome_snvs:
grch37:
v1.4:
file: whole_genome_SNVs.tsv.gz
file_check: whole_genome_SNVs.tsv.gz.md5
file_index: whole_genome_SNVs.tsv.gz.tbi
file_index_check: whole_genome_SNVs.tsv.gz.tbi.md5
outfile: grch37_cadd_whole_genome_snvs_-v1.4-.tsv.gz
outfile_check: grch37_cadd_whole_genome_snvs_-v1.4-.tsv.gz.md5
outfile_check_method: md5sum
outfile_index: grch37_cadd_whole_genome_snvs_-v1.4-.tsv.gz.tbi
outfile_index_check: grch37_cadd_whole_genome_snvs_-v1.4-.tsv.gz.tbi.md5
outfile_index_check_method: md5sum
url_prefix: https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh37/
v1.6:
file: whole_genome_SNVs.tsv.gz
file_check: whole_genome_SNVs.tsv.gz.md5
outfile: grch37_cadd_whole_genome_snvs_-v1.6-.tsv.gz
outfile_check: grch37_cadd_whole_genome_snvs_-v1.6-.tsv.gz.md5
outfile_check_method: md5sum
url_prefix: https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh37/
grch38:
v1.5:
file: whole_genome_SNVs.tsv.gz
file_check: whole_genome_SNVs.tsv.gz.md5
file_index: whole_genome_SNVs.tsv.gz.tbi
file_index_check: whole_genome_SNVs.tsv.gz.tbi.md5
outfile: grch38_cadd_whole_genome_snvs_-v1.5-.tsv.gz
outfile_check: grch38_cadd_whole_genome_snvs_-v1.5-.tsv.gz.md5
outfile_check_method: md5sum
outfile_index: grch38_cadd_whole_genome_snvs_-v1.5-.tsv.gz.tbi
outfile_index_check: grch38_cadd_whole_genome_snvs_-v1.5-.tsv.gz.tbi.md5
outfile_index_check_method: md5sum
url_prefix: https://krishna.gs.washington.edu/download/CADD/v1.5/GRCh38/
v1.6:
file: whole_genome_SNVs.tsv.gz
file_check: whole_genome_SNVs.tsv.gz.md5
outfile: grch38_cadd_whole_genome_snvs_-v1.6-.tsv.gz
outfile_check: grch38_cadd_whole_genome_snvs_-v1.6-.tsv.gz.md5
outfile_check_method: md5sum
url_prefix: https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh38/
chromograph_cytoband:
grch37:
v1.0:
file: grch37_cytoband.bed
file_check: grch37_cytoband.bed.md5
outfile: grch37_cytoband.bed
outfile_check: grch37_cytoband.bed.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/
grch38:
v1.0:
file: grch38_cytoband.bed
file_check: grch38_cytoband.bed.md5
outfile: grch38_cytoband.bed
outfile_check: grch38_cytoband.bed.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/
clinvar:
grch37:
20211010:
file: clinvar_20211010.vcf.gz
file_check: clinvar_20211010.vcf.gz.md5
file_index: clinvar_20211010.vcf.gz.tbi
outfile: grch37_clinvar_-20211010-.vcf.gz
outfile_check: grch37_clinvar_-20211010-.vcf.gz.md5
outfile_index: grch37_clinvar_-20211010-.vcf.gz.tbi
outfile_check_method: md5sum
url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
20220829:
file: clinvar_20220829.vcf.gz
file_check: clinvar_20220829.vcf.gz.md5
file_index: clinvar_20220829.vcf.gz.tbi
outfile: grch37_clinvar_-20220829-.vcf.gz
outfile_check: grch37_clinvar_-20220829-.vcf.gz.md5
outfile_index: grch37_clinvar_-20220829-.vcf.gz.tbi
outfile_check_method: md5sum
url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
grch38:
20211010:
file: clinvar_20211010.vcf.gz
file_check: clinvar_20211010.vcf.gz.md5
file_index: clinvar_20211010.vcf.gz.tbi
outfile: grch38_clinvar_-20211010-.vcf.gz
outfile_check: grch38_clinvar_-20211010-.vcf.gz.md5
outfile_index: grch38_clinvar_-20211010-.vcf.gz.tbi
outfile_check_method: md5sum
url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
20220829:
file: clinvar_20220829.vcf.gz
file_check: clinvar_20220829.vcf.gz.md5
file_index: clinvar_20220829.vcf.gz.tbi
outfile: grch38_clinvar_-20220829-.vcf.gz
outfile_check: grch38_clinvar_-20220829-.vcf.gz.md5
outfile_index: grch38_clinvar_-20220829-.vcf.gz.tbi
outfile_check_method: md5sum
url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
dbnsfp:
grch37:
3.5a:
file: dbNSFPv3.5a.zip
outfile: grch37_dbnsfp_-v3.5a-.zip
url_prefix: ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/
outfile_decompress: unzip
grch38:
4.1a:
file: dbNSFP4.1a.zip
outfile: grch38_dbnsfp_-4.1a-.zip
outfile_decompress: unzip
url_prefix: ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/
4.3a:
file: dbNSFP4.3a.zip
outfile: grch38_dbnsfp_-4.3a-.zip
outfile_decompress: unzip
url_prefix: ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/
dbsnp:
grch37:
138_esa_129:
file: dbsnp_138.b37.excluding_sites_after_129.vcf.gz
file_check: dbsnp_138.b37.excluding_sites_after_129.vcf.gz.md5
file_index: dbsnp_138.b37.excluding_sites_after_129.vcf.idx.gz
file_index_check: dbsnp_138.b37.excluding_sites_after_129.vcf.idx.gz.md5
outfile: grch37_dbsnp_-138_esa_129-.vcf.gz
outfile_check: grch37_dbsnp_-138_esa_129-.vcf.gz.md5
outfile_index: grch37_dbsnp_-138_esa_129-.vcf.idx.gz
outfile_index_check: grch37_dbsnp_-138_esa_129-.vcf.idx.gz.md5
outfile_decompress: gzip
outfile_index_decompress: gzip
outfile_check_method: md5sum
outfile_index_check_method: md5sum
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
138:
file: dbsnp_138.b37.vcf.gz
file_check: dbsnp_138.b37.vcf.gz.md5
file_index: dbsnp_138.b37.vcf.idx.gz
file_index_check: dbsnp_138.b37.vcf.idx.gz.md5
outfile: grch37_dbsnp_-138-.vcf.gz
outfile_check: grch37_dbsnp_-138-.vcf.gz.md5
outfile_index: grch37_dbsnp_-138-.vcf.idx.gz
outfile_index_check: grch37_dbsnp_-138-.vcf.idx.gz.md5
outfile_decompress: gzip
outfile_index_decompress: gzip
outfile_check_method: md5sum
outfile_index_check_method: md5sum
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
grch38:
gold_standard_dbsnp:
file: Homo_sapiens_assembly38.variantEvalGoldStandard.vcf.gz
file_index: Homo_sapiens_assembly38.variantEvalGoldStandard.vcf.gz.tbi
outfile: grch38_variant_-gold_standard_dbsnp-.vcf.gz
outfile_decompress: gzip
outfile_index: grch38_variant_-gold_standard_dbsnp-.vcf.gz.tbi
url_prefix: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/beta/
user: gsapubftp-anonymous
138:
file: Homo_sapiens_assembly38.dbsnp138.vcf
file_index: Homo_sapiens_assembly38.dbsnp138.vcf.idx
outfile: grch38_dbsnp_-138-.vcf
outfile_index: grch38_dbsnp_-138-.vcf.idx
url_prefix: https://storage.googleapis.com/gcp-public-data--broad-references/hg38/v0/
146:
file: dbsnp_146.hg38.vcf.gz
file_index: dbsnp_146.hg38.vcf.gz.tbi
outfile: grch38_dbsnp_-146-.vcf.gz
outfile_decompress: gzip
outfile_index: grch38_dbsnp_-146-.vcf.gz.tbi
url_prefix: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/
user: gsapubftp-anonymous
delly_exclude:
grch37:
20200310: # latest commit for file on master branch
file: human.hg19.excl.tsv
outfile: hg19_human_excl_-20200310-.tsv
url_prefix: https://raw.githubusercontent.com/dellytools/delly/master/excludeTemplates/
grch38:
20150915: # latest commit for file on master branch
file: human.hg38.excl.tsv
outfile: grch38_human_excl_-20150915-.tsv
url_prefix: https://raw.githubusercontent.com/dellytools/delly/master/excludeTemplates/
expansionhunter:
grch37:
4.0.2:
file: variant_catalog_grch37.json
file_check: variant_catalog_grch37.json.md5
outfile: grch37_expansionhunter_variant_catalog_-4.0.2-.json
outfile_check: grch37_expansionhunter_variant_catalog_-4.0.2-.json.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v4.0.2/
5.0.0:
file: variant_catalog_grch37.json
file_check: variant_catalog_grch37.json.md5
outfile: grch37_expansionhunter_variant_catalog_-5.0.0-.json
outfile_check: grch37_expansionhunter_variant_catalog_-5.0.0-.json.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/
grch38:
4.0.2:
file: variant_catalog_hg38.json
file_check: variant_catalog_hg38.json.md5
outfile: grch38_expansionhunter_variant_catalog_-4.0.2-.json
outfile_check: grch38_expansionhunter_variant_catalog_-4.0.2-.json.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v4.0.2/
5.0.0:
file: variant_catalog_hg38.json
file_check: variant_catalog_hg38.json.md5
outfile: grch38_expansionhunter_variant_catalog_-5.0.0-.json
outfile_check: grch38_expansionhunter_variant_catalog_-5.0.0-.json.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/
gatk_mitochondrial_ref:
grch38:
v0_m_amb:
file: Homo_sapiens_assembly38.chrM.fasta.amb
outfile: grch38_homo_sapiens_-v0_m-.fasta.amb
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_ann:
file: Homo_sapiens_assembly38.chrM.fasta.ann
outfile: grch38_homo_sapiens_-v0_m-.fasta.ann
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_blacklist:
file: blacklist_sites.hg38.chrM.bed
file_index: blacklist_sites.hg38.chrM.bed.idx
outfile: grch38_homo_sapiens_blacklist_sites_-v0_m-.bed
outfile_index: grch38_homo_sapiens_blacklist_sites_-v0_m-.bed.idx
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_blacklist_shifted:
file: blacklist_sites.hg38.chrM.shifted_by_8000_bases.fixed.bed
file_index: blacklist_sites.hg38.chrM.shifted_by_8000_bases.fixed.bed.idx
outfile: grch38_homo_sapiens_blacklist_sites_shifted_-v0_m-.bed
outfile_index: grch38_homo_sapiens_blacklist_sites_shifted_-v0_m-.bed.idx
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_bwt:
file: Homo_sapiens_assembly38.chrM.fasta.bwt
outfile: grch38_homo_sapiens_-v0_m-.fasta.bwt
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_control_shifted_interval_list:
file: control_region_shifted.chrM.interval_list
outfile: grch38_homo_sapiens_control_shifted_-v0_m-.interval_list
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_dict:
file: Homo_sapiens_assembly38.chrM.dict
outfile: grch38_homo_sapiens_-v0_m-.dict
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_fasta:
file: Homo_sapiens_assembly38.chrM.fasta
file_index: Homo_sapiens_assembly38.chrM.fasta.fai
outfile: grch38_homo_sapiens_-v0_m-.fasta
outfile_index: grch38_homo_sapiens_-v0_m-.fasta.fai
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_non_control_interval_list:
file: non_control_region.chrM.interval_list
outfile: grch38_homo_sapiens_non_control_-v0_m-.interval_list
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_numt_interval_list:
file: chrMWithFinalNuMTs.hg38.interval_list
outfile: grch38_homo_sapiens_numt_-v0_m-.interval_list
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_pac:
file: Homo_sapiens_assembly38.chrM.fasta.pac
outfile: grch38_homo_sapiens_-v0_m-.fasta.pac
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_sa:
file: Homo_sapiens_assembly38.chrM.fasta.sa
outfile: grch38_homo_sapiens_-v0_m-.fasta.sa
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_shiftback:
file: ShiftBack.chain
outfile: grch38_homo_sapiens_shiftback_-v0_m-.chain
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_shifted_amb:
file: Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.amb
outfile: grch38_homo_sapiens_shifted_-v0_m-.fasta.amb
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_shifted_ann:
file: Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.ann
outfile: grch38_homo_sapiens_shifted_-v0_m-.fasta.ann
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_shifted_bwt:
file: Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt
outfile: grch38_homo_sapiens_shifted_-v0_m-.fasta.bwt
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_shifted_dict:
file: Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.dict
outfile: grch38_homo_sapiens_shifted_-v0_m-.dict
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_shifted_fasta:
file: Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta
file_index: Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.fai
outfile: grch38_homo_sapiens_shifted_-v0_m-.fasta
outfile_index: grch38_homo_sapiens_shifted_-v0_m-.fasta.fai
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_shifted_pac:
file: Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac
outfile: grch38_homo_sapiens_shifted_-v0_m-.fasta.pac
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
v0_m_shifted_sa:
file: Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa
outfile: grch38_homo_sapiens_shifted_-v0_m-.fasta.sa
url_prefix: https://storage.googleapis.com/broad-references/hg38/v0/chrM/
genbank_haplogroup:
grch37:
20150801:
file: grch37_genbank_haplogroup_-2015-08-01-.vcf.gz
file_check: grch37_genbank_haplogroup_-2015-08-01-.vcf.gz.md5
file_index: grch37_genbank_haplogroup_-2015-08-01-.vcf.gz.tbi
file_index_check: grch37_genbank_haplogroup_-2015-08-01-.vcf.gz.tbi.md5
outfile: grch37_genbank_haplogroup_-2015-08-01-.vcf.gz
outfile_check: grch37_genbank_haplogroup_-2015-08-01-.vcf.gz.md5
outfile_check_method: md5sum
outfile_index: grch37_genbank_haplogroup_-2015-08-01-.vcf.gz.tbi
outfile_index_check: grch37_genbank_haplogroup_-2015-08-01-.vcf.gz.tbi.md5
outfile_index_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/frequency/
genomic_superdups:
grch37:
20181009:
file: genomicSuperDups.txt.gz
outfile: grch37_genomics_super_dups_-20181009-.txt.gz
outfile_decompress: gzip
url_prefix: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
grch38:
20190826:
file: genomicSuperDups.txt.gz
outfile: grch38_genomics_super_dups_-20190826-.txt.gz
outfile_decompress: gzip
url_prefix: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/
giab:
grch37:
na12878_v2.19_bed:
file: union13callableMQonlymerged_addcert_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs_v2.19_2mindatasets_5minYesNoRatio.bed.gz
outfile: grch37_nist_hg001_-na12878_v2.19-.bed.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv2.19/
na12878_v2.19_wgs:
file: NISTIntegratedCalls_14datasets_131103_allcall_UGHapMerge_HetHomVarPASS_VQSRv2.19_2mindatasets_5minYesNoRatio_all_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs.vcf.gz
outfile: grch37_nist_hg001_-na12878_v2.19-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv2.19/
na12878_v3.3.2_bed:
file: HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel.bed
outfile: grch37_nist_hg001_-na12878_v3.3.2-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/
na12878_v3.3.2_wgs:
file: HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf.gz
outfile: grch37_nist_hg001_-na12878_v3.3.2-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh37/
na12878_v4.2.1_bed:
file: HG001_GRCh37_1_22_v4.2.1_benchmark.bed
outfile: grch37_nist_hg001_-na12878_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh37/
na12878_v4.2.1_wgs:
file: HG001_GRCh37_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG001_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch37_nist_hg001_-na12878_v4.2.1-.vcf.gz
outfile_index: grch37_nist_hg001_-na12878_v4.2.1-.vcf.gz
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh37/
na24143_v3.3.2_bed:
file: HG004_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed
outfile: grch37_nist_hg004_-na24143_v3.3.2-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh37/
na24143_v3.3.2_wgs:
file: HG004_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X_CHROM1-22_v.3.3.2_highconf.vcf.gz
outfile: grch37_nist_hg004_-na24143_v3.3.2-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh37/
na24143_v4.2.1_bed:
file: HG004_GRCh37_1_22_v4.2.1_benchmark_noinconsistent.bed
outfile: grch37_nist_hg004_-na24143_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv4.2.1/GRCh37/
na24143_v4.2.1_wgs:
file: HG004_GRCh37_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG004_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch37_nist_hg004_-na24143_v4.2.1-.vcf.gz
outfile_index: grch37_nist_hg004_-na24143_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv4.2.1/GRCh37/
na24385_v3.3.2_bed:
file: HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed
outfile: grch37_nist_hg002_-na24385_v3.3.2-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh37/
na24385_v3.3.2_wgs:
file: HG002_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz
outfile: grch37_nist_hg002_-na24385_v3.3.2-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh37/
na24385_v4.2.1_bed:
file: HG002_GRCh37_1_22_v4.2.1_benchmark_noinconsistent.bed
outfile: grch37_nist_hg002_-na24385_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh37/
na24385_v4.2.1_wgs:
file: HG002_GRCh37_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG002_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch37_nist_hg002_-na24385_v4.2.1-.vcf.gz
outfile_index: grch37_nist_hg002_-na24385_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh37/
na24149_v4.2.1_bed:
file: HG003_GRCh37_1_22_v4.2.1_benchmark.bed
outfile: grch37_nist_hg003_-na24149_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh37/
na24149_v4.2.1_wgs:
file: HG003_GRCh37_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG003_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch37_nist_hg003_-na24149_v4.2.1-.vcf.gz
outfile_index: grch37_nist_hg003_-na24149_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh37/
na24631_v3.3.2_bed:
file: HG005_GRCh37_highconf_CG-IllFB-IllGATKHC-Ion-SOLID_CHROM1-22_v.3.3.2_highconf_noMetaSV.bed
outfile: grch37_nist_hg005_-na24631_v3.3.2-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/
na24631_v3.3.2_wgs:
file: HG005_GRCh37_highconf_CG-IllFB-IllGATKHC-Ion-SOLID_CHROM1-22_v.3.3.2_highconf.vcf.gz
outfile: grch37_nist_hg005_-na24631_v3.3.2-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh37/
na24631_v4.2.1_bed:
file: HG005_GRCh37_1_22_v4.2.1_benchmark.bed
outfile: grch37_nist_hg005_-na24631_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh37/
na24631_v4.2.1_wgs:
file: HG005_GRCh37_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG005_GRCh37_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch37_nist_hg005_-na24631_v4.2.1-.vcf.gz
outfile_index: grch37_nist_hg005_-na24631_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh37/
grch38:
na12878_v3.3.2_bed:
file: HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed
outfile: grch38_nist_hg001_-na12878_v3.3.2-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh38/
na12878_v3.3.2_wgs:
file: HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf.gz
outfile: grch38_nist_hg001_-na12878_v3.3.2-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh38/
na12878_v4.2.1_bed:
file: HG001_GRCh38_1_22_v4.2.1_benchmark.bed
outfile: grch38_nist_hg001_-na12878_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/
na12878_v4.2.1_wgs:
file: HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch38_nist_hg001_-na12878_v4.2.1-.vcf.gz
outfile_index: grch38_nist_hg001_-na12878_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/
na24143_v3.3.2_bed:
file: HG004_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed
outfile: grch38_nist_hg004_-na24143_v3.3.2-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh38/
na24143_v3.3.2_wgs:
file: HG004_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC_CHROM1-22_v.3.3.2_highconf.vcf.gz
outfile: grch38_nist_hg004_-na24143_v3.3.2-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh38/
na24143_v4.2.1_bed:
file: HG004_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
outfile: grch38_nist_hg004_-na24143_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv4.2.1/GRCh38/
na24143_v4.2.1_wgs:
file: HG004_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.vcf.gz
file_index: HG004_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.vcf.gz.tbi
outfile: grch38_nist_hg004_-na24143_v4.2.1-.vcf.gz
outfile_index: grch38_nist_hg004_-na24143_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv4.2.1/GRCh38/
na24385_v3.3.2_bed:
file: HG002_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf_noinconsistent.bed
outfile: grch38_nist_hg002_-na24385_v3.3.2-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh38/
na24385_v3.3.2_wgs:
file: HG002_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf_triophased.vcf.gz
outfile: grch38_nist_hg002_-na24385_v3.3.2-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh38/
na24385_v4.2.1_bed:
file: HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
outfile: grch38_nist_hg002_-na24385_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/
na24385_v4.2.1_wgs:
file: HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch38_nist_hg002_-na24385_v4.2.1-.vcf.gz
outfile_index: grch38_nist_hg002_-na24385_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/
na24149_v4.2.1_bed:
file: HG003_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
outfile: grch38_nist_hg003_-na24149_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/
na24149_v4.2.1_wgs:
file: HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG003_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch38_nist_hg003_-na24149_v4.2.1-.vcf.gz
outfile_index: grch38_nist_hg003_-na24149_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv4.2.1/GRCh38/
na24631_v3.3.2_bed:
file: HG005_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf.bed
outfile: grch38_nist_hg005_-na24631_v3.3.2-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh38/
na24631_v3.3.2_wgs:
file: HG005_GRCh38_GIAB_highconf_CG-Illfb-IllsentieonHC-Ion-10XsentieonHC-SOLIDgatkHC_CHROM1-22_v.3.3.2_highconf.vcf.gz
outfile: grch38_nist_hg005_-na24631_v3.3.2-.vcf.gz
outfile_decompress: gzip
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh38/
na24631_v4.2.1_bed:
file: HG005_GRCh38_1_22_v4.2.1_benchmark.bed
outfile: grch38_nist_hg005_-na24631_v4.2.1-.bed
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh38/
na24631_v4.2.1_wgs:
file: HG005_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
file_index: HG005_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi
outfile: grch38_nist_hg005_-na24631_v4.2.1-.vcf.gz
outfile_index: grch38_nist_hg005_-na24631_v4.2.1-.vcf.gz.tbi
url_prefix: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv4.2.1/GRCh38/
gnomad:
grch37:
r2.0.1:
file: gnomad.genomes.r2.0.1.sites.noVEP.vcf.gz
file_index: gnomad.genomes.r2.0.1.sites.noVEP.vcf.gz.tbi
outfile: grch37_gnomad.genomes_-r2.0.1-.vcf.gz
outfile_index: grch37_gnomad.genomes_-r2.0.1-.vcf.gz.tbi
url_prefix: ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh37/variation_genotype/
r2.1.1:
file: gnomad.genomes.r2.1.1.sites.vcf.bgz
file_index: gnomad.genomes.r2.1.1.sites.vcf.bgz.tbi
outfile: grch37_gnomad.genomes_-r2.1.1-.vcf.gz
outfile_index: grch37_gnomad.genomes_-r2.1.1-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/genomes/
r2.1.1_sv:
file: gnomad_v2_sv.sites.vcf.gz
file_index: gnomad_v2_sv.sites.vcf.gz.tbi
outfile: grch37_gnomad.genomes_-r2.1.1_sv-.vcf.gz
outfile_index: grch37_gnomad.genomes_-r2.1.1_sv-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/gnomad-public/papers/2019-sv/
grch38:
r2.1.1:
file: gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz
file_index: gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz.tbi
outfile: grch38_gnomad.genomes_liftover-r2.1.1-.vcf.gz
outfile_index: grch38_gnomad.genomes_liftover-r2.1.1-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/gnomad-public/release/2.1.1/liftover_grch38/vcf/genomes/
gnomad_chrsplit:
grch38:
r3.1.1:
file: gnomad.genomes.v3.1.1.sites.chr{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y}.vcf.bgz
file_index: gnomad.genomes.v3.1.1.sites.chr{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y}.vcf.bgz.tbi
outfile: grch38_gnomad_reformated_-r3.1.1-.vcf.gz
outfile_index: grch38_gnomad_reformated_-r3.1.1-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1.1/vcf/genomes/
r3.1.2:
file: gnomad.genomes.v3.1.2.sites.chr{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y}.vcf.bgz
file_index: gnomad.genomes.v3.1.2.sites.chr{1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y}.vcf.bgz.tbi
outfile: grch38_gnomad_reformated_-r3.1.2-.vcf.gz
outfile_index: grch38_gnomad_reformated_-r3.1.2-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1.2/vcf/genomes/
gnomad_mt:
grch37:
r3.1:
file: gnomad.genomes.v3.1.sites.chrM.vcf.bgz
file_index: gnomad.genomes.v3.1.sites.chrM.vcf.bgz.tbi
outfile: grch37_gnomad_genomes_mt_-r3.1-.vcf.gz
outfile_index: grch37_gnomad_genomes_mt_-r3.1-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1/vcf/genomes/
grch38:
r3.1:
file: gnomad.genomes.v3.1.sites.chrM.vcf.bgz
file_index: gnomad.genomes.v3.1.sites.chrM.vcf.bgz.tbi
outfile: grch38_gnomad_genomes_mt_-r3.1-.vcf.gz
outfile_index: grch38_gnomad_genomes_mt_-r3.1-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1/vcf/genomes/
gnomad_pli_per_gene:
grch37:
r2.1.1:
file: gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz
outfile: gnomad_lof_metrics_per_gene_-r2.1.1-.txt.gz
outfile_decompress: gzip
url_prefix: https://storage.googleapis.com/gnomad-public/release/2.1.1/constraint/
hapmap:
grch37:
3.3:
file: hapmap_3.3.b37.vcf.gz
file_check: hapmap_3.3.b37.vcf.gz.md5
file_index: hapmap_3.3.b37.vcf.idx.gz
file_index_check: hapmap_3.3.b37.vcf.idx.gz.md5
outfile: grch37_hapmap_-3.3-.vcf.gz
outfile_check: grch37_hapmap_-3.3-.vcf.gz.md5
outfile_index: grch37_hapmap_-3.3-.vcf.idx.gz
outfile_index_check: grch37_hapmap_-3.3-.vcf.idx.gz.md5
outfile_decompress: gzip
outfile_index_decompress: gzip
outfile_check_method: md5sum
outfile_index_check_method: md5sum
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
grch38:
3.3:
file: hapmap_3.3.hg38.vcf.gz
file_index: hapmap_3.3.hg38.vcf.gz.tbi
outfile: grch38_hapmap_-3.3-.vcf.gz
outfile_index: grch38_hapmap_-3.3-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
manta_call_regions:
grch38:
1.0:
file: grch38_manta_call_regions_-1.0-.bed.gz
file_check: grch38_manta_call_regions_-1.0-.bed.gz.md5
file_index: grch38_manta_call_regions_-1.0-.bed.gz.tbi
file_index_check: grch38_manta_call_regions_-1.0-.bed.gz.tbi.md5
outfile: grch38_manta_call_regions_-1.0-.bed.gz
outfile_check: grch38_manta_call_regions_-1.0-.bed.gz.md5
outfile_check_method: md5sum
outfile_index: grch38_manta_call_regions_-1.0-.bed.gz.tbi
outfile_index_check: grch38_manta_call_regions_-1.0-.bed.gz.tbi.md5
outfile_index_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/
mills_and_1000g_indels:
grch37:
gold_standard_indels:
file: Mills_and_1000G_gold_standard.indels.b37.vcf.gz
file_check: Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5
file_index: Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz
file_index_check: Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz.md5
outfile: grch37_mills_and_1000g_-gold_standard_indels-.vcf.gz
outfile_check: grch37_mills_and_1000g_-gold_standard_indels-.vcf.gz.md5
outfile_index: grch37_mills_and_1000g_-gold_standard_indels-.vcf.idx.gz
outfile_index_check: grch37_mills_and_1000g_-gold_standard_indels-.vcf.idx.gz.md5
outfile_decompress: gzip
outfile_index_decompress: gzip
outfile_check_method: md5sum
outfile_index_check_method: md5sum
url_prefix: https://storage.googleapis.com/gatk-legacy-bundles/b37/
grch38:
gold_standard_indels:
file: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
file_index: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
outfile: grch38_mills_and_1000g_-gold_standard_indels-.vcf.gz
outfile_index: grch38_mills_and_1000g_-gold_standard_indels-.vcf.gz.tbi
url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
rank_model:
grch37:
v1.33:
file: rank_model_-v1.33-.ini
file_check: rank_model_-v1.33-.ini.md5
outfile: rank_model_-v1.33-.ini
outfile_check: rank_model_-v1.33-.ini.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
v1.34:
file: rank_model_-v1.34-.ini
file_check: rank_model_-v1.34-.ini.md5
outfile: rank_model_-v1.34-.ini
outfile_check: rank_model_-v1.34-.ini.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
grch38:
v0.2:
file: grch38_rank_model_-v0.2-.ini
file_check: grch38_rank_model_-v0.2-.ini.md5
outfile: grch38_rank_model_-v0.2-.ini
outfile_check: grch38_rank_model_-v0.-.ini.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
reduced_penetrance:
grch37:
2017:
file: grch37_cust003-cmms-red-pen_-2017-.tsv
file_check: grch37_cust003-cmms-red-pen_-2017-.tsv.md5
outfile: grch37_cust003-cmms-red-pen_-2017-.tsv
outfile_check: grch37_cust003-cmms-red-pen_-2017-.tsv.md5
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/gene_panel/
scout_exons:
grch37:
201701:
file: grch37_scout_exons_-2017-01-.bed
file_check: grch37_scout_exons_-2017-01-.bed.md5
outfile: grch37_scout_exons_-2017-01-.bed
outfile_check: grch37_scout_exons_-2017-01-.bed.md5
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/gene_panel/
grch38:
200917:
file: grch38_scout_exons_-2020-09-17-.bed
file_check: grch38_scout_exons_-2020-09-17-.bed.md5
outfile: grch38_scout_exons_-2020-09-17-.bed
outfile_check: grch378_scout_exons_-2020-09-17-.bed.md5
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/gene_panel/
sv_vcfanno_config:
grch37:
v1.3:
file: grch37_sv_vcfanno_config_-v1.3-.toml
file_check: grch37_sv_vcfanno_config_-v1.3-.toml.md5
outfile: grch37_sv_vcfanno_config_-v1.3-.toml
outfile_check: grch37_sv_vcfanno_config_-v1.3-.toml.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
v1.4:
file: grch37_sv_vcfanno_config_-v1.4-.toml
file_check: grch37_sv_vcfanno_config_-v1.4-.toml.md5
outfile: grch37_sv_vcfanno_config_-v1.4-.toml
outfile_check: grch37_sv_vcfanno_config_-v1.4-.toml.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
grch38:
v0.2:
file: grch38_sv_vcfanno_config_-v0.2-.toml
file_check: grch38_sv_vcfanno_config_-v0.2-.toml.md5
outfile: grch38_sv_vcfanno_config_-v0.2-.toml
outfile_check: grch38_sv_vcfanno_config_-v0.2-.toml.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
svrank_model:
grch37:
v1.8:
file: svrank_model_-v1.8-.ini
file_check: svrank_model_-v1.8-.ini.md5
outfile: svrank_model_-v1.8-.ini
outfile_check: svrank_model_-v1.8-.ini.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
v1.9:
file: svrank_model_-v1.9-.ini
file_check: svrank_model_-v1.9-.ini.md5
outfile: svrank_model_-v1.9-.ini
outfile_check: svrank_model_-v1.9-.ini.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
grch38:
v0.1:
file: grch38_sv_rank_model_-v0.1-.ini
file_check: grch38_sv_rank_model_-v0.1-.ini.md5
outfile: grch38_sv_rank_model_-v0.1-.ini
outfile_check: grch38_sv_rank_model_-v0.1-.ini.md5
outfile_check_method: md5sum
url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
vcf2cytosure_blacklist_regions:
grch37:
1.0:
file: grch37_cytosure_blacklist_-1.0-.bed
file_check: grch37_cytosure_blacklist_-1.0-.bed.md5