366afa4a74c46ec6fb2b667a2902a873feec40cf max Mon Apr 20 23:00:05 2026 -0700 varFreqsAll: rebuild combined bigBed to include GA4K and CoLoRSdb Regenerate the All Databases Combined track with the two long-read PacBio subtracks (GA4K 552 samples and CoLoRSdb v1.2.0 1,027 samples) that were added to varFreqs since the March build. Source count rises from 21 to 23 databases; final bigBed is 37.7 GB with 1.17B records and 113 fields. Updates varFreqs.ra filterValues.sources and per- database AF/AC filters for the two new sources, and databases.tsv + varFreqs.txt (build notes). refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 341609e63e4..e336ad0a36c 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,484 +1,492 @@ track varFreqs shortLabel Variant Frequencies 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 # 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 + 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 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.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 + filterByRange.GA4KAF on + filterLabel.GA4KAF GA4K PacBio LR AF + filterByRange.CoLoRSdbAF on + filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR 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 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 + filterByRange.GA4KAC on + filterLabel.GA4KAC GA4K PacBio LR AC + filterByRange.CoLoRSdbAC on + filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR 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 #bigDataUrl /gbdb/$D/varFreqs/me/me.freq.vcf.gz #visibility pack #type vcfTabix #hapClusterEnabled true #dataVersion 10/04/2023, v1.1.3 #tableBrowser off #priority 1 track topmed shortLabel NHLBI TOPMED 10 151k WGS longLabel Variant Frequencies: NHLBI TOPMED - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/topmed/topmed10.vcf.gz dataVersion Freeze 10 visibility pack priority 2 track sfariSparkExomes shortLabel SFARI Spark 140k WES longLabel Variant Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 visibility pack priority 2.5 track sfariSparkWgs shortLabel SFARI Spark 12k WGS longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 visibility pack priority 2.5 html sfariSparkExomes #track mcps #shortLabel Mexico City Prospective Study 10k WGS+141k WES #longLabel Variant Frequencies: Mexico City Prospective Study (MCPS) #tableBrowser off #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) #priority 3 track tommo60kjpn shortLabel Japan ToMMO 61k WGS longLabel Variant Frequencies: Japan 61k - ToMMO SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility pack dataVersion 2025-06-16 priority 5 track alfaVcf shortLabel NCBI ALFA 408k WGS/WES/array longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz visibility pack dataVersion R4 priority 4.1 url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track finngen parent varFreqs on visibility pack type vcfTabix shortLabel Finland FinnGen 500k imputed longLabel Variant Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track swefreq parent varFreqs on visibility pack type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel Variant Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$D/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track mgrb shortLabel Australia MGRB 4k WGS longLabel Variant Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 visibility pack # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia Pilot Subs 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility pack track gaspIndel shortLabel GenomeAsia Pilot Indels 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/All.indels.annot.cont_withmaf.vcf.gz visibility pack html gasp track abraom shortLabel Brazil ABraOM 1k WGS longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility pack 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/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility pack track kova shortLabel Korea KOVA 1.9k WGS+3.5k WES longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.5k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/kova/kova.v7.vcf.gz visibility pack 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 bigDataUrl /gbdb/$D/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility pack tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS longLabel Variant Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz visibility pack dataVersion r1.1 track saudi shortLabel Saudi Genome Project 302 WGS longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility pack track schema shortLabel SCHEMA Schizophrenia 121k WES longLabel Variant Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility pack dataVersion 2022 priority 4.9 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track mxbFreq shortLabel Mexico Biobank 6k Array longLabel Variant Frequencies: Mexico Biobank - 6,011 individuals, genotyping array type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mxb/mxb.freq.vcf.gz visibility pack dataVersion Nov 2025 (hg38 lift) priority 6 track sgdpFreq shortLabel SGDP 279 WGS longLabel Variant Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility pack dataVersion 2016-12-07 (hg38 lift) priority 7 track gregor shortLabel GREGoR R4 3.6k WGS longLabel Variant Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz visibility pack dataVersion R04 (Oct 2025) priority 8 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS longLabel Variant Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz visibility pack dataVersion v3.1.2 priority 8 track ga4kSnv shortLabel GA4K 552 PacBio LR longLabel Variant Frequencies: Genomic Answers for Kids (Children's Mercy) - 552 PacBio HiFi long-read WGS (pediatric rare-disease cohort) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz visibility pack priority 9 track colorsDbSnv shortLabel CoLoRSdb 1,027 LR SNVs/indels longLabel Variant Frequencies: CoLoRSdb v1.2.0 - 1,027 long-read PacBio HiFi WGS, DeepVariant+GLnexus joint-called SNVs and small indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz visibility pack dataVersion v1.2.0 priority 9.5