165a15d6a94d53f8162a01e69f3912a7a23a3b50 max Mon Mar 23 06:47:55 2026 -0700 mostly done with the variant frequencies track, refs#36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 25947fab34a..0f7a4cdbe9c 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -3,129 +3,235 @@ longLabel Variant Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on track varFreqsAll shortLabel All Databases Combined 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 - filterValues.sources aou|AllOfUs,spk|SPARK_iWES,wgs|SFARI_WGS,ga|GenomeAsia100K,kov|KOVA,tom|ToMMo,mcp|MCPS,ind|IndiGenomes,fin|FinnGen,sau|Saudi,swe|SweGen,top|TOPMed,abr|ABraOM + # 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 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 + filterLabel.totalAC Total Allele Count (all databases) # Per-database AF filters - filterByRange.aouAF on - filterLabel.aouAF AllOfUs AF - filterByRange.spkAF on - filterLabel.spkAF SPARK AF - filterByRange.wgsAF on - filterLabel.wgsAF SFARI WGS AF - filterByRange.gaAF on - filterLabel.gaAF GenomeAsia AF - filterByRange.kovAF on - filterLabel.kovAF KOVA AF - filterByRange.tomAF on - filterLabel.tomAF ToMMo AF - filterByRange.mcpAF on - filterLabel.mcpAF MCPS AF - filterByRange.indAF on - filterLabel.indAF IndiGenomes AF - filterByRange.finAF on - filterLabel.finAF FinnGen AF - filterByRange.sauAF on - filterLabel.sauAF Saudi AF - filterByRange.sweAF on - filterLabel.sweAF SweGen AF - filterByRange.topAF on - filterLabel.topAF TOPMed AF - filterByRange.abrAF on - filterLabel.abrAF ABraOM AF + filterByRange.AllOfUsAF on + filterLabel.AllOfUsAF AllOfUs AF + filterByRange.SPARKAF on + filterLabel.SPARKAF SPARK WES AF + filterByRange.SFARI_WGSAF on + filterLabel.SFARI_WGSAF SFARI WGS AF + filterByRange.GenomeAsiaAF on + filterLabel.GenomeAsiaAF GenomeAsia SNVs AF + filterByRange.GenomeAsiaIndelAF on + filterLabel.GenomeAsiaIndelAF GenomeAsia Indels AF + filterByRange.KOVAAF on + filterLabel.KOVAAF KOVA Korea AF + filterByRange.ToMMoAF on + filterLabel.ToMMoAF ToMMo Japan AF + filterByRange.IndiGenAF on + filterLabel.IndiGenAF IndiGenomes India AF + filterByRange.FinnGenAF on + filterLabel.FinnGenAF FinnGen Finland AF + filterByRange.SaudiAF on + filterLabel.SaudiAF Saudi AF + filterByRange.SweGenAF on + filterLabel.SweGenAF SweGen Sweden AF + filterByRange.TOPMedAF on + filterLabel.TOPMedAF TOPMed AF + filterByRange.ABraOMAF on + filterLabel.ABraOMAF ABraOM Brazil AF + filterByRange.ALFAAF on + filterLabel.ALFAAF ALFA AF + filterByRange.MGRBAF on + filterLabel.MGRBAF MGRB Australia AF + filterByRange.HRCAF on + 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 # Per-database AC filters - filterByRange.aouAC on - filterLabel.aouAC AllOfUs AC - filterByRange.spkAC on - filterLabel.spkAC SPARK AC - filterByRange.wgsAC on - filterLabel.wgsAC SFARI WGS AC - filterByRange.gaAC on - filterLabel.gaAC GenomeAsia AC - filterByRange.kovAC on - filterLabel.kovAC KOVA AC - filterByRange.tomAC on - filterLabel.tomAC ToMMo AC - filterByRange.mcpAC on - filterLabel.mcpAC MCPS AC - filterByRange.indAC on - filterLabel.indAC IndiGenomes AC - filterByRange.finAC on - filterLabel.finAC FinnGen AC - filterByRange.sauAC on - filterLabel.sauAC Saudi AC - filterByRange.sweAC on - filterLabel.sweAC SweGen AC - filterByRange.topAC on - filterLabel.topAC TOPMed AC - filterByRange.abrAC on - filterLabel.abrAC ABraOM AC - # Population-specific AF filters (AllOfUs) - filterByRange.aouAF_AFR on - filterLabel.aouAF_AFR AllOfUs AFR AF - filterByRange.aouAF_AMR on - filterLabel.aouAF_AMR AllOfUs AMR AF - filterByRange.aouAF_EAS on - filterLabel.aouAF_EAS AllOfUs EAS AF - filterByRange.aouAF_EUR on - filterLabel.aouAF_EUR AllOfUs EUR AF - filterByRange.aouAF_SAS on - filterLabel.aouAF_SAS AllOfUs SAS AF - # Population-specific AF filters (GenomeAsia) - filterByRange.gaAF_NEA on - filterLabel.gaAF_NEA GenomeAsia NEA AF - filterByRange.gaAF_SEA on - filterLabel.gaAF_SEA GenomeAsia SEA AF - filterByRange.gaAF_SAS on - filterLabel.gaAF_SAS GenomeAsia SAS AF - # Population-specific AF filters (MCPS) - filterByRange.mcpAF_AFR on - filterLabel.mcpAF_AFR MCPS AFR AF - filterByRange.mcpAF_EUR on - filterLabel.mcpAF_EUR MCPS EUR AF - filterByRange.mcpAF_IMX on - filterLabel.mcpAF_IMX MCPS Indigenous MX AF - priority 0.1 + 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 + filterByRange.IndiGenAC on + filterLabel.IndiGenAC IndiGenomes India AC + filterByRange.FinnGenAC on + filterLabel.FinnGenAC FinnGen Finland AC + filterByRange.SaudiAC on + filterLabel.SaudiAC Saudi AC + filterByRange.SweGenAC on + filterLabel.SweGenAC SweGen Sweden AC + filterByRange.TOPMedAC on + filterLabel.TOPMedAC TOPMed AC + filterByRange.ABraOMAC on + filterLabel.ABraOMAC ABraOM Brazil AC + filterByRange.ALFAAC on + filterLabel.ALFAAC ALFA AC + filterByRange.MGRBAC on + filterLabel.MGRBAC MGRB Australia AC + filterByRange.HRCAC on + 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 + # 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 + filterLabel.AllOfUsAC_AFR AllOfUs African AC + filterByRange.AllOfUsAC_AMR on + filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC + filterByRange.AllOfUsAC_EAS on + filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC + filterByRange.AllOfUsAC_EUR on + filterLabel.AllOfUsAC_EUR AllOfUs European AC + filterByRange.AllOfUsAC_OCE on + filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC + filterByRange.AllOfUsAC_SAS on + filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC + # GenomeAsia SNVs populations + filterByRange.GenomeAsiaAF_NEA on + filterLabel.GenomeAsiaAF_NEA GenomeAsia SNVs Northeast Asian AF + filterByRange.GenomeAsiaAF_SEA on + filterLabel.GenomeAsiaAF_SEA GenomeAsia SNVs Southeast Asian AF + filterByRange.GenomeAsiaAF_SAS on + filterLabel.GenomeAsiaAF_SAS GenomeAsia SNVs South Asian AF + filterByRange.GenomeAsiaAC_NEA on + filterLabel.GenomeAsiaAC_NEA GenomeAsia SNVs Northeast Asian AC + filterByRange.GenomeAsiaAC_SEA on + filterLabel.GenomeAsiaAC_SEA GenomeAsia SNVs Southeast Asian AC + filterByRange.GenomeAsiaAC_SAS on + filterLabel.GenomeAsiaAC_SAS GenomeAsia SNVs South Asian AC + # gnomAD HGDP+1kG populations + filterByRange.HGDP1kGAF_afr on + filterLabel.HGDP1kGAF_afr gnomAD HGDP+1kG African AF + filterByRange.HGDP1kGAF_ami on + filterLabel.HGDP1kGAF_ami gnomAD HGDP+1kG Amish AF + filterByRange.HGDP1kGAF_amr on + filterLabel.HGDP1kGAF_amr gnomAD HGDP+1kG Latino AF + filterByRange.HGDP1kGAF_asj on + filterLabel.HGDP1kGAF_asj gnomAD HGDP+1kG Ashkenazi Jewish AF + filterByRange.HGDP1kGAF_eas on + filterLabel.HGDP1kGAF_eas gnomAD HGDP+1kG East Asian AF + filterByRange.HGDP1kGAF_fin on + filterLabel.HGDP1kGAF_fin gnomAD HGDP+1kG Finnish AF + filterByRange.HGDP1kGAF_mid on + filterLabel.HGDP1kGAF_mid gnomAD HGDP+1kG Middle Eastern AF + filterByRange.HGDP1kGAF_nfe on + filterLabel.HGDP1kGAF_nfe gnomAD HGDP+1kG European AF + filterByRange.HGDP1kGAF_oth on + filterLabel.HGDP1kGAF_oth gnomAD HGDP+1kG Other AF + filterByRange.HGDP1kGAF_sas on + filterLabel.HGDP1kGAF_sas gnomAD HGDP+1kG South Asian AF + filterByRange.HGDP1kGAC_afr on + filterLabel.HGDP1kGAC_afr gnomAD HGDP+1kG African AC + filterByRange.HGDP1kGAC_ami on + filterLabel.HGDP1kGAC_ami gnomAD HGDP+1kG Amish AC + filterByRange.HGDP1kGAC_amr on + filterLabel.HGDP1kGAC_amr gnomAD HGDP+1kG Latino AC + filterByRange.HGDP1kGAC_asj on + filterLabel.HGDP1kGAC_asj gnomAD HGDP+1kG Ashkenazi Jewish AC + filterByRange.HGDP1kGAC_eas on + filterLabel.HGDP1kGAC_eas gnomAD HGDP+1kG East Asian AC + filterByRange.HGDP1kGAC_fin on + filterLabel.HGDP1kGAC_fin gnomAD HGDP+1kG Finnish AC + filterByRange.HGDP1kGAC_mid on + filterLabel.HGDP1kGAC_mid gnomAD HGDP+1kG Middle Eastern AC + filterByRange.HGDP1kGAC_nfe on + filterLabel.HGDP1kGAC_nfe gnomAD HGDP+1kG European AC + filterByRange.HGDP1kGAC_oth on + filterLabel.HGDP1kGAC_oth gnomAD HGDP+1kG Other AC + filterByRange.HGDP1kGAC_sas on + filterLabel.HGDP1kGAC_sas gnomAD HGDP+1kG South Asian AC + # GREGoR populations + filterByRange.GREGoRAF_AFF on + filterLabel.GREGoRAF_AFF GREGoR Affected AF + filterByRange.GREGoRAF_UNA on + filterLabel.GREGoRAF_UNA GREGoR Unaffected AF + filterByRange.GREGoRAF_UNK on + filterLabel.GREGoRAF_UNK GREGoR Unknown AF + filterByRange.GREGoRAC_AFF on + filterLabel.GREGoRAC_AFF GREGoR Affected AC + filterByRange.GREGoRAC_UNA on + filterLabel.GREGoRAC_UNA GREGoR Unaffected AC + filterByRange.GREGoRAC_UNK on + filterLabel.GREGoRAC_UNK GREGoR Unknown AC + skipEmptyFields on track allofus shortLabel AllOfUs v7 245k WGS longLabel Variant Frequencies: AllOfUs - v7 245k WGS, only with allele count >= 20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility pack priority 0.5 #track me #shortLabel Regeneron Million Exomes 983k WES #longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on