0a5389e8b81efa99e932f5e9e2424b27ce1af095 max Sun May 17 14:53:57 2026 -0700 varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index e746bcd3e2c..cd63c958f36 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -12,31 +12,31 @@ type bigBed 9 + parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_all/varFreqsAll.bb visibility pack itemRgb on maxWindowToDraw 5000000 priority 0.1 mouseOver <b>Var:</b> $name<br><b>AA change:</b> $aaChange<br><b>Var type:</b> $varType<br><b>Conseq:</b> $consequence<br><b>Max AF:</b> $maxAF<br><b>Total AC:</b> $totalAC<br><b>Sources:</b> $sources # Variant type and consequence filters filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence # Source database filter - filterValues.sources AllOfUs|AllOfUs,SPARK|SPARK WES,SFARI_WGS|SFARI WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,KOVA|KOVA Korea,ToMMo|ToMMo Japan,IndiGen|IndiGenomes India,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,MexBB|Mexico Biobank,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,NPM|NPM Singapore + filterValues.sources AllOfUs|AllOfUs,SPARK|SPARK WES,SFARI_WGS|SFARI WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,KOVA|KOVA Korea,ToMMo|ToMMo Japan,IndiGen|IndiGenomes India,GenomeIndia|GenomeIndia 9.7k WGS,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,MexBB|Mexico Biobank,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,NPM|NPM Singapore filterType.sources multipleListOr filterLabel.sources Source Database # Length filters filterByRange.refLen on filterLabel.refLen Reference Length filterByRange.altLen on filterLabel.altLen Alternate Length filterByRange.varLen on filterLabel.varLen Length Change # Max AF filter filterByRange.maxAF on filterLabel.maxAF Max Allele Frequency filterLimits.maxAF 0:1 # Total AC filter filterByRange.totalAC on @@ -82,30 +82,32 @@ filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF (4k cohort) filterByRange.GREGoRAF on filterLabel.GREGoRAF GREGoR AF filterByRange.SCHEMAAF on filterLabel.SCHEMAAF SCHEMA AF filterByRange.GA4KAF on filterLabel.GA4KAF GA4K PacBio LR AF filterByRange.CoLoRSdbAF on filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR AF filterByRange.SVatalogAF on filterLabel.SVatalogAF SVatalog 101 10XG SR AF filterByRange.Tishkoff180AF on filterLabel.Tishkoff180AF Tishkoff 180 African WGS AF filterByRange.NPMAF on filterLabel.NPMAF NPM Singapore AF + filterByRange.GenomeIndiaAF on + filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF # Per-database AC filters filterByRange.AllOfUsAC on filterLabel.AllOfUsAC AllOfUs AC filterByRange.SPARKAC on filterLabel.SPARKAC SPARK WES AC filterByRange.SFARI_WGSAC on filterLabel.SFARI_WGSAC SFARI WGS AC filterByRange.GenomeAsiaAC on filterLabel.GenomeAsiaAC GenomeAsia SNVs AC filterByRange.GenomeAsiaIndelAC on filterLabel.GenomeAsiaIndelAC GenomeAsia Indels AC filterByRange.KOVAAC on filterLabel.KOVAAC KOVA Korea AC filterByRange.ToMMoAC on filterLabel.ToMMoAC ToMMo Japan AC @@ -135,30 +137,32 @@ filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC (4k cohort) filterByRange.GREGoRAC on filterLabel.GREGoRAC GREGoR AC filterByRange.SCHEMAAC on filterLabel.SCHEMAAC SCHEMA AC filterByRange.GA4KAC on filterLabel.GA4KAC GA4K PacBio LR AC filterByRange.CoLoRSdbAC on filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR AC filterByRange.SVatalogAC on filterLabel.SVatalogAC SVatalog 101 10XG SR AC filterByRange.Tishkoff180AC on filterLabel.Tishkoff180AC Tishkoff 180 African WGS AC filterByRange.NPMAC on filterLabel.NPMAC NPM Singapore AC + filterByRange.GenomeIndiaAC on + filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC # Population-specific AF filters # AllOfUs local-ancestry populations # NB: these are local-ancestry-stratified frequencies (per-position, per-haplotype-class), # NOT the AllOfUs paper's global Rye ancestry categories. See varFreqs.html for details. filterByRange.AllOfUsAF_AFR on filterLabel.AllOfUsAF_AFR AllOfUs African AF (local ancestry) filterByRange.AllOfUsAF_AMR on filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF (local ancestry) filterByRange.AllOfUsAF_EAS on filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF (local ancestry) filterByRange.AllOfUsAF_EUR on filterLabel.AllOfUsAF_EUR AllOfUs European AF (local ancestry) filterByRange.AllOfUsAF_OCE on filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF (local ancestry) filterByRange.AllOfUsAF_SAS on @@ -465,30 +469,40 @@ type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility dense dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS longLabel Variant Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility dense dataVersion IndiGen pilot (Jain 2021) + track genomeindia + shortLabel India GenomeIndia 9.7k WGS + longLabel Variant Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/_genomeindia/genomeindia.vcf.gz + visibility dense + dataVersion 9768GI_SummaryStats (Apr 2025) + priority 4.8 + track kova shortLabel Korea KOVA 5.3k mixed longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz visibility dense tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on