37a5b97198453bd06cb03d2092cae239f368e84c max Wed Apr 29 05:49:14 2026 -0700 varFreqs: add tishkoff180 subtrack (Fan et al. 2023, 180 indigenous African WGS, hg19 lift) Sites-only SNP VCF with aggregate AC/AF/AN from 180 individuals (15 each from 12 populations across Ethiopia, Tanzania, Cameroon, Botswana), sequenced at >30x on HiSeq X Ten. hg19 calls supplied by the Tishkoff lab (UPenn) and lifted to hg38 with CrossMap. Redistribution is not permitted, so tableBrowser is disabled. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>, refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 62550f60d7b..1c8e57e7c18 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -11,31 +11,31 @@ longLabel Variant Frequencies: All Databases Combined with Consequence Annotations type bigBed 9 + parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/varFreqsAll.bb visibility dense itemRgb on maxWindowToDraw 5000000 priority 0.1 #mouseOver $aaChange $dnaChange # 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,.|Intergenic 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 + 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 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 @@ -75,30 +75,32 @@ filterLabel.HRCAF HRC AF filterByRange.MexBBAF on filterLabel.MexBBAF Mexico Biobank AF filterByRange.SGDPAF on filterLabel.SGDPAF SGDP AF filterByRange.HGDP1kGAF on filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF 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 # 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 @@ -122,30 +124,32 @@ filterLabel.HRCAC HRC AC filterByRange.MexBBAC on filterLabel.MexBBAC Mexico Biobank AC filterByRange.SGDPAC on filterLabel.SGDPAC SGDP AC filterByRange.HGDP1kGAC on filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC 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 # Population-specific AF filters # AllOfUs populations filterByRange.AllOfUsAF_AFR on filterLabel.AllOfUsAF_AFR AllOfUs African AF filterByRange.AllOfUsAF_AMR on filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF filterByRange.AllOfUsAF_EAS on filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF filterByRange.AllOfUsAF_EUR on filterLabel.AllOfUsAF_EUR AllOfUs European AF filterByRange.AllOfUsAF_OCE on filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF filterByRange.AllOfUsAF_SAS on filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF filterByRange.AllOfUsAC_AFR on @@ -487,15 +491,26 @@ parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz visibility pack dataVersion v1.2.0 priority 9.5 track svatalogSnv shortLabel SVatalog 101 WGS longLabel Variant Frequencies: GWAS SVatalog SNPs from 101 Samples (Chirmade 2026, 10X Genomics linked short-reads) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz visibility pack priority 10 + track tishkoff180 + shortLabel Indigenous Africans 180 WGS + longLabel Variant Frequencies: 180 WGS from 12 Indigenous African Populations (Fan/Tishkoff 2023, lifted from hg19) + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/tishkoff/tishkoff180.vcf.gz + visibility pack + dataVersion Cell 2023 (hg19 lift) + tableBrowser off + priority 7.5 +