f674b74547b883a2054c4771533d753266e07c06 lrnassar Mon May 4 16:21:54 2026 -0700 QA pass on varFreqs supertrack: relabel HGDP+1kG and AllOfUs per-population fields to match data semantics, expose all 7 GenomeAsia populations in filter UI, normalize labels and capitalization, add Methods + References to description page, and flag GenomeAsia GRCh37 coordinate mismatch via dataVersion. refs #36642 trackDb (varFreqs.ra): - HGDP+1kG per-population AC/AF labels relabeled from "gnomAD HGDP+1kG <pop>" to "gnomAD v3.1.2 <pop> (full release)" since the values come from the full ~76k-genome gnomAD release, not the 4,094-genome HGDP+1kG cohort. - AllOfUs per-population AC/AF labels appended with "(local ancestry)" to clarify these are local-ancestry-stratified haplotype frequencies (Ioannidis lab pipeline), not the AllOfUs paper's global Rye categories. - Added 8 new filter entries for GenomeAsia OCE/AMR/AFR/WER (data has 7 population groups; trackUI previously exposed only 3). - shortLabel shortenings: alfaVcf, finngen, gasp, gaspIndel, kova, saudi, schema, colorsDbSnv, tishkoff180. - longLabel shortenings: ga4kSnv, colorsDbSnv, svatalogSnv, tishkoff180. - Capitalization fixes: SFARI Spark to SFARI SPARK, Japan ToMMO to Japan ToMMo, NHLBI TOPMED to NHLBI TOPMed. - dataVersion added on 6 subtracks that lacked it (gasp, gaspIndel, indigenomes, saudi, ga4kSnv, svatalogSnv); gasp/gaspIndel flagged "Pilot 2019 (GRCh37 - to be lifted)" for visibility of the open hg19 issue. - Default visibility flipped: non-summary subtracks now dense, summary varFreqsAll now pack. Container stays hide. Description page (varFreqs.html): - Added References section with 21 primary publications for the source cohorts. - Added "Notes on Specific Sub-tracks" explaining the HGDP+1kG cohort vs full-release distinction and the AllOfUs locAncFreq semantics. - Added Methods section describing per-subtrack and combined-track build pipelines, with links to the GitHub scripts directory and makedoc. - Encoded genome@soe.ucsc.edu with encodeEmail.pl. - Corrected "more than 1.2 billion variants" to "1.17 billion" (actual varFreqsAll.bb itemCount: 1,169,063,801). - Normalized body-text quotes to " entities. - AllOfUs and HGDP+1kG rows in the datasets table now flag the semantic distinction inline. Build config (scripts/varFreqs/populations.tsv): - Added 4 GenomeAsia rows (OCE, AMR, AFR, WER) so the next varFreqsAll bigBed rebuild will populate the new filter columns. - Fixed HGDP1kG nfe label "European" to "Non-Finnish European" to match the trackdb relabel. diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 1c8e57e7c18..339c35c94f8 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,516 +1,542 @@ 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 + visibility pack 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,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 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 + 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 # 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 + 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 # Population-specific AF filters - # AllOfUs populations + # 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 + filterLabel.AllOfUsAF_AFR AllOfUs African AF (local ancestry) filterByRange.AllOfUsAF_AMR on - filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF + filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF (local ancestry) filterByRange.AllOfUsAF_EAS on - filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF + filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF (local ancestry) filterByRange.AllOfUsAF_EUR on - filterLabel.AllOfUsAF_EUR AllOfUs European AF + filterLabel.AllOfUsAF_EUR AllOfUs European AF (local ancestry) filterByRange.AllOfUsAF_OCE on - filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF + filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF (local ancestry) filterByRange.AllOfUsAF_SAS on - filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF + filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF (local ancestry) filterByRange.AllOfUsAC_AFR on - filterLabel.AllOfUsAC_AFR AllOfUs African AC + filterLabel.AllOfUsAC_AFR AllOfUs African AC (local ancestry) filterByRange.AllOfUsAC_AMR on - filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC + filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC (local ancestry) filterByRange.AllOfUsAC_EAS on - filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC + filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC (local ancestry) filterByRange.AllOfUsAC_EUR on - filterLabel.AllOfUsAC_EUR AllOfUs European AC + filterLabel.AllOfUsAC_EUR AllOfUs European AC (local ancestry) filterByRange.AllOfUsAC_OCE on - filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC + filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC (local ancestry) filterByRange.AllOfUsAC_SAS on - filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC - # GenomeAsia SNVs populations + filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC (local ancestry) + # GenomeAsia SNVs populations (7 groups in source VCF) 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.GenomeAsiaAF_OCE on + filterLabel.GenomeAsiaAF_OCE GenomeAsia SNVs Oceanian AF + filterByRange.GenomeAsiaAF_AMR on + filterLabel.GenomeAsiaAF_AMR GenomeAsia SNVs American AF + filterByRange.GenomeAsiaAF_AFR on + filterLabel.GenomeAsiaAF_AFR GenomeAsia SNVs African AF + filterByRange.GenomeAsiaAF_WER on + filterLabel.GenomeAsiaAF_WER GenomeAsia SNVs Western European Ref 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.GenomeAsiaAC_OCE on + filterLabel.GenomeAsiaAC_OCE GenomeAsia SNVs Oceanian AC + filterByRange.GenomeAsiaAC_AMR on + filterLabel.GenomeAsiaAC_AMR GenomeAsia SNVs American AC + filterByRange.GenomeAsiaAC_AFR on + filterLabel.GenomeAsiaAC_AFR GenomeAsia SNVs African AC + filterByRange.GenomeAsiaAC_WER on + filterLabel.GenomeAsiaAC_WER GenomeAsia SNVs Western European Ref AC + # gnomAD HGDP+1kG: per-population AF/AC values are from the FULL gnomAD v3.1.2 + # release (~76k genomes), not the 4,094-genome HGDP+1kG cohort. Only the + # cohort-level HGDP1kGAF / HGDP1kGAC fields above reflect the 4k-cohort. filterByRange.HGDP1kGAF_afr on - filterLabel.HGDP1kGAF_afr gnomAD HGDP+1kG African AF + filterLabel.HGDP1kGAF_afr gnomAD v3.1.2 African AF (full release) filterByRange.HGDP1kGAF_ami on - filterLabel.HGDP1kGAF_ami gnomAD HGDP+1kG Amish AF + filterLabel.HGDP1kGAF_ami gnomAD v3.1.2 Amish AF (full release) filterByRange.HGDP1kGAF_amr on - filterLabel.HGDP1kGAF_amr gnomAD HGDP+1kG Latino AF + filterLabel.HGDP1kGAF_amr gnomAD v3.1.2 Latino AF (full release) filterByRange.HGDP1kGAF_asj on - filterLabel.HGDP1kGAF_asj gnomAD HGDP+1kG Ashkenazi Jewish AF + filterLabel.HGDP1kGAF_asj gnomAD v3.1.2 Ashkenazi Jewish AF (full release) filterByRange.HGDP1kGAF_eas on - filterLabel.HGDP1kGAF_eas gnomAD HGDP+1kG East Asian AF + filterLabel.HGDP1kGAF_eas gnomAD v3.1.2 East Asian AF (full release) filterByRange.HGDP1kGAF_fin on - filterLabel.HGDP1kGAF_fin gnomAD HGDP+1kG Finnish AF + filterLabel.HGDP1kGAF_fin gnomAD v3.1.2 Finnish AF (full release) filterByRange.HGDP1kGAF_mid on - filterLabel.HGDP1kGAF_mid gnomAD HGDP+1kG Middle Eastern AF + filterLabel.HGDP1kGAF_mid gnomAD v3.1.2 Middle Eastern AF (full release) filterByRange.HGDP1kGAF_nfe on - filterLabel.HGDP1kGAF_nfe gnomAD HGDP+1kG European AF + filterLabel.HGDP1kGAF_nfe gnomAD v3.1.2 Non-Finnish European AF (full release) filterByRange.HGDP1kGAF_oth on - filterLabel.HGDP1kGAF_oth gnomAD HGDP+1kG Other AF + filterLabel.HGDP1kGAF_oth gnomAD v3.1.2 Other AF (full release) filterByRange.HGDP1kGAF_sas on - filterLabel.HGDP1kGAF_sas gnomAD HGDP+1kG South Asian AF + filterLabel.HGDP1kGAF_sas gnomAD v3.1.2 South Asian AF (full release) filterByRange.HGDP1kGAC_afr on - filterLabel.HGDP1kGAC_afr gnomAD HGDP+1kG African AC + filterLabel.HGDP1kGAC_afr gnomAD v3.1.2 African AC (full release) filterByRange.HGDP1kGAC_ami on - filterLabel.HGDP1kGAC_ami gnomAD HGDP+1kG Amish AC + filterLabel.HGDP1kGAC_ami gnomAD v3.1.2 Amish AC (full release) filterByRange.HGDP1kGAC_amr on - filterLabel.HGDP1kGAC_amr gnomAD HGDP+1kG Latino AC + filterLabel.HGDP1kGAC_amr gnomAD v3.1.2 Latino AC (full release) filterByRange.HGDP1kGAC_asj on - filterLabel.HGDP1kGAC_asj gnomAD HGDP+1kG Ashkenazi Jewish AC + filterLabel.HGDP1kGAC_asj gnomAD v3.1.2 Ashkenazi Jewish AC (full release) filterByRange.HGDP1kGAC_eas on - filterLabel.HGDP1kGAC_eas gnomAD HGDP+1kG East Asian AC + filterLabel.HGDP1kGAC_eas gnomAD v3.1.2 East Asian AC (full release) filterByRange.HGDP1kGAC_fin on - filterLabel.HGDP1kGAC_fin gnomAD HGDP+1kG Finnish AC + filterLabel.HGDP1kGAC_fin gnomAD v3.1.2 Finnish AC (full release) filterByRange.HGDP1kGAC_mid on - filterLabel.HGDP1kGAC_mid gnomAD HGDP+1kG Middle Eastern AC + filterLabel.HGDP1kGAC_mid gnomAD v3.1.2 Middle Eastern AC (full release) filterByRange.HGDP1kGAC_nfe on - filterLabel.HGDP1kGAC_nfe gnomAD HGDP+1kG European AC + filterLabel.HGDP1kGAC_nfe gnomAD v3.1.2 Non-Finnish European AC (full release) filterByRange.HGDP1kGAC_oth on - filterLabel.HGDP1kGAC_oth gnomAD HGDP+1kG Other AC + filterLabel.HGDP1kGAC_oth gnomAD v3.1.2 Other AC (full release) filterByRange.HGDP1kGAC_sas on - filterLabel.HGDP1kGAC_sas gnomAD HGDP+1kG South Asian AC + filterLabel.HGDP1kGAC_sas gnomAD v3.1.2 South Asian AC (full release) # 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 + longLabel Variant Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 - visibility pack + visibility dense 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/$D/varFreqs/me/me.freq.vcf.gz #visibility pack #type vcfTabix #hapClusterEnabled true #dataVersion 10/04/2023, v1.1.3 #tableBrowser off #priority 1 track topmed - shortLabel NHLBI TOPMED 10 151k WGS - longLabel Variant Frequencies: NHLBI TOPMED - 151k WGS + shortLabel NHLBI TOPMed 10 151k WGS + longLabel Variant Frequencies: NHLBI TOPMed - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/topmed/topmed10.vcf.gz dataVersion Freeze 10 - visibility pack + visibility dense priority 2 track sfariSparkExomes - shortLabel SFARI Spark 140k WES + shortLabel SFARI SPARK 140k WES longLabel Variant Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 - visibility pack + visibility dense priority 2.5 track sfariSparkWgs - shortLabel SFARI Spark 12k WGS + shortLabel SFARI SPARK 12k WGS longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 - visibility pack + visibility dense 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/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) #priority 3 track tommo60kjpn - shortLabel Japan ToMMO 61k WGS - longLabel Variant Frequencies: Japan 61k - ToMMO SNV+Indels + shortLabel Japan ToMMo 61k WGS + longLabel Variant Frequencies: Japan 61k - ToMMo SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz - visibility pack + visibility dense dataVersion 2025-06-16 priority 5 track alfaVcf - shortLabel NCBI ALFA 408k WGS/WES/array + shortLabel NCBI ALFA 408k mixed 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 + visibility dense 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 + visibility dense type vcfTabix - shortLabel Finland FinnGen 500k imputed + shortLabel FinnGen R12 500k imputed longLabel Variant Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track swefreq parent varFreqs on - visibility pack + visibility dense type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel Variant Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$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/$D/varFreqs/mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 - visibility pack + visibility dense # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp - shortLabel GenomeAsia Pilot Subs 1.7k WGS + shortLabel GenomeAsia 1.7k SNVs longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz - visibility pack + visibility dense + dataVersion Pilot 2019 (GRCh37 - to be lifted) track gaspIndel - shortLabel GenomeAsia Pilot Indels 1.7k WGS + shortLabel GenomeAsia 1.7k Indels longLabel Variant Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/All.indels.annot.cont_withmaf.vcf.gz - visibility pack + visibility dense + dataVersion Pilot 2019 (GRCh37 - to be lifted) html gasp track abraom shortLabel Brazil ABraOM 1k WGS longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz - visibility pack + 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/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz - visibility pack + visibility dense + dataVersion IndiGen pilot (Jain 2021) track kova - shortLabel Korea KOVA 1.9k WGS+3.5k WES + shortLabel Korea KOVA 5.3k mixed longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.5k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/kova/kova.v7.vcf.gz - visibility pack + 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 bigDataUrl /gbdb/$D/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz - visibility pack + visibility dense tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS longLabel Variant Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz - visibility pack + visibility dense dataVersion r1.1 track saudi - shortLabel Saudi Genome Project 302 WGS + shortLabel Saudi Genome 302 WGS longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz - visibility pack + visibility dense + dataVersion SHGP (figshare 51297884, 2025) track schema - shortLabel SCHEMA Schizophrenia 121k WES + shortLabel SCHEMA 121k WES Sz longLabel Variant Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz - visibility pack + visibility dense 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/$D/varFreqs/mxb/mxb.freq.vcf.gz - visibility pack + visibility dense dataVersion Nov 2025 (hg38 lift) priority 6 track sgdpFreq shortLabel SGDP 279 WGS longLabel Variant Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz - visibility pack + visibility dense 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/$D/varFreqs/gregor/gregor.vcf.gz - visibility pack + visibility dense dataVersion R04 (Oct 2025) priority 8 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS longLabel Variant Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz - visibility pack + visibility dense 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) + longLabel Variant Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz - visibility pack + visibility dense + dataVersion Cohen 2022 release priority 9 track colorsDbSnv - shortLabel CoLoRSdb 1,027 LR SNVs/indels - longLabel Variant Frequencies: CoLoRSdb v1.2.0 - 1,027 long-read PacBio HiFi WGS, DeepVariant+GLnexus joint-called SNVs and small indels + shortLabel CoLoRSdb 1k LR SNV/Ind + longLabel Variant Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz - visibility pack + visibility dense 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) + longLabel Variant Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz - visibility pack + visibility dense + dataVersion Chirmade 2025 release priority 10 track tishkoff180 - shortLabel Indigenous Africans 180 WGS - longLabel Variant Frequencies: 180 WGS from 12 Indigenous African Populations (Fan/Tishkoff 2023, lifted from hg19) + shortLabel 12 Afr Pops 180 WGS + longLabel Variant Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tishkoff/tishkoff180.vcf.gz - visibility pack + visibility dense dataVersion Cell 2023 (hg19 lift) tableBrowser off priority 7.5