3180d71425ab40bc022712bb95868bfe80747375
max
Fri May 29 08:52:38 2026 -0700
[Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll
#Preview2 week - bugs introduced now will need a build patch to fix
Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the
SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus
AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control
sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease
(SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI,
MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main
combined track is purely WGS/WES.
Build scripts parameterized so the same code drives all three combined
builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py
gains --databases-file / --populations-file and a per-track autoSql table
name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in
PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails).
refs #36642
diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra
index 1c43df781e0..fe9150102f5 100644
--- src/hg/makeDb/trackDb/human/varFreqs.ra
+++ src/hg/makeDb/trackDb/human/varFreqs.ra
@@ -1,664 +1,825 @@
track varFreqs
shortLabel SNV Frequencies
longLabel SNV 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/_all/varFreqsAll.bb
visibility pack
itemRgb on
maxWindowToDraw 5000000
priority 0.1
mouseOver Var: $name
AA change: $aaChange
Var type: $varType
Conseq: $consequence
Max AF: $maxAF
Total AC: $totalAC
Sources: $sources
# Source database filter
- filterValues.sources AllOfUs|AllOfUs,SPARK|SPARK WES,SFARI_WGS|SFARI WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,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,WBBC|WBBC China,TPMI|TPMI Taiwan,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR
+ filterValues.sources AllOfUs|AllOfUs,SPARK|SPARK WES,SFARI_WGS|SFARI WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,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,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR
filterType.sources multipleListOr
filterLabel.sources Source Database
# 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
# 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.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 (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.WBBCAF on
filterLabel.WBBCAF WBBC China AF
- filterByRange.TPMIAF on
- filterLabel.TPMIAF TPMI Taiwan AF
filterByRange.ChinaMAPAF on
filterLabel.ChinaMAPAF China ChinaMAP AF
filterByRange.GenomeIndiaAF on
filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF
filterByRange.GoNLAF on
filterLabel.GoNLAF GoNL Netherlands ~13x 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.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 (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.WBBCAC on
filterLabel.WBBCAC WBBC China AC
- filterByRange.TPMIAC on
- filterLabel.TPMIAC TPMI Taiwan AC
filterByRange.ChinaMAPAC on
filterLabel.ChinaMAPAC China ChinaMAP AC
filterByRange.GenomeIndiaAC on
filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC
filterByRange.GoNLAC on
filterLabel.GoNLAC GoNL Netherlands ~13x SR 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
filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF (local ancestry)
filterByRange.AllOfUsAC_AFR on
filterLabel.AllOfUsAC_AFR AllOfUs African AC (local ancestry)
filterByRange.AllOfUsAC_AMR on
filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC (local ancestry)
filterByRange.AllOfUsAC_EAS on
filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC (local ancestry)
filterByRange.AllOfUsAC_EUR on
filterLabel.AllOfUsAC_EUR AllOfUs European AC (local ancestry)
filterByRange.AllOfUsAC_OCE on
filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC (local ancestry)
filterByRange.AllOfUsAC_SAS on
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
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 v3.1.2 African AF (full release)
filterByRange.HGDP1kGAF_ami on
filterLabel.HGDP1kGAF_ami gnomAD v3.1.2 Amish AF (full release)
filterByRange.HGDP1kGAF_amr on
filterLabel.HGDP1kGAF_amr gnomAD v3.1.2 Latino AF (full release)
filterByRange.HGDP1kGAF_asj on
filterLabel.HGDP1kGAF_asj gnomAD v3.1.2 Ashkenazi Jewish AF (full release)
filterByRange.HGDP1kGAF_eas on
filterLabel.HGDP1kGAF_eas gnomAD v3.1.2 East Asian AF (full release)
filterByRange.HGDP1kGAF_fin on
filterLabel.HGDP1kGAF_fin gnomAD v3.1.2 Finnish AF (full release)
filterByRange.HGDP1kGAF_mid on
filterLabel.HGDP1kGAF_mid gnomAD v3.1.2 Middle Eastern AF (full release)
filterByRange.HGDP1kGAF_nfe on
filterLabel.HGDP1kGAF_nfe gnomAD v3.1.2 Non-Finnish European AF (full release)
filterByRange.HGDP1kGAF_oth on
filterLabel.HGDP1kGAF_oth gnomAD v3.1.2 Other AF (full release)
filterByRange.HGDP1kGAF_sas on
filterLabel.HGDP1kGAF_sas gnomAD v3.1.2 South Asian AF (full release)
filterByRange.HGDP1kGAC_afr on
filterLabel.HGDP1kGAC_afr gnomAD v3.1.2 African AC (full release)
filterByRange.HGDP1kGAC_ami on
filterLabel.HGDP1kGAC_ami gnomAD v3.1.2 Amish AC (full release)
filterByRange.HGDP1kGAC_amr on
filterLabel.HGDP1kGAC_amr gnomAD v3.1.2 Latino AC (full release)
filterByRange.HGDP1kGAC_asj on
filterLabel.HGDP1kGAC_asj gnomAD v3.1.2 Ashkenazi Jewish AC (full release)
filterByRange.HGDP1kGAC_eas on
filterLabel.HGDP1kGAC_eas gnomAD v3.1.2 East Asian AC (full release)
filterByRange.HGDP1kGAC_fin on
filterLabel.HGDP1kGAC_fin gnomAD v3.1.2 Finnish AC (full release)
filterByRange.HGDP1kGAC_mid on
filterLabel.HGDP1kGAC_mid gnomAD v3.1.2 Middle Eastern AC (full release)
filterByRange.HGDP1kGAC_nfe on
filterLabel.HGDP1kGAC_nfe gnomAD v3.1.2 Non-Finnish European AC (full release)
filterByRange.HGDP1kGAC_oth on
filterLabel.HGDP1kGAC_oth gnomAD v3.1.2 Other AC (full release)
filterByRange.HGDP1kGAC_sas on
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
# NPM Singapore ancestry groups
filterByRange.NPMAF_Chinese on
filterLabel.NPMAF_Chinese NPM Singapore Chinese AF
filterByRange.NPMAF_Malay on
filterLabel.NPMAF_Malay NPM Singapore Malay AF
filterByRange.NPMAF_Indian on
filterLabel.NPMAF_Indian NPM Singapore Indian AF
filterByRange.NPMAC_Chinese on
filterLabel.NPMAC_Chinese NPM Singapore Chinese AC
filterByRange.NPMAC_Malay on
filterLabel.NPMAC_Malay NPM Singapore Malay AC
filterByRange.NPMAC_Indian on
filterLabel.NPMAC_Indian NPM Singapore Indian AC
# WBBC China populations
filterByRange.WBBCAF_North on
filterLabel.WBBCAF_North WBBC North Han AF
filterByRange.WBBCAF_Central on
filterLabel.WBBCAF_Central WBBC Central Han AF
filterByRange.WBBCAF_South on
filterLabel.WBBCAF_South WBBC South Han AF
filterByRange.WBBCAF_Lingnan on
filterLabel.WBBCAF_Lingnan WBBC Lingnan Han AF
filterByRange.WBBCAC_North on
filterLabel.WBBCAC_North WBBC North Han AC
filterByRange.WBBCAC_Central on
filterLabel.WBBCAC_Central WBBC Central Han AC
filterByRange.WBBCAC_South on
filterLabel.WBBCAC_South WBBC South Han AC
filterByRange.WBBCAC_Lingnan on
filterLabel.WBBCAC_Lingnan WBBC Lingnan Han AC
+ # SFARI SPARK WES autism phenotype split (asd column of individuals_registration)
+ filterByRange.SPARKAF_AUT on
+ filterLabel.SPARKAF_AUT SPARK WES ASD proband AF
+ filterByRange.SPARKAF_NON_AUT on
+ filterLabel.SPARKAF_NON_AUT SPARK WES Non-ASD family AF
+ filterByRange.SPARKAC_AUT on
+ filterLabel.SPARKAC_AUT SPARK WES ASD proband AC
+ filterByRange.SPARKAC_NON_AUT on
+ filterLabel.SPARKAC_NON_AUT SPARK WES Non-ASD family AC
+ # SFARI SPARK WGS autism phenotype split
+ filterByRange.SFARI_WGSAF_AUT on
+ filterLabel.SFARI_WGSAF_AUT SFARI WGS ASD proband AF
+ filterByRange.SFARI_WGSAF_NON_AUT on
+ filterLabel.SFARI_WGSAF_NON_AUT SFARI WGS Non-ASD family AF
+ filterByRange.SFARI_WGSAC_AUT on
+ filterLabel.SFARI_WGSAC_AUT SFARI WGS ASD proband AC
+ filterByRange.SFARI_WGSAC_NON_AUT on
+ filterLabel.SFARI_WGSAC_NON_AUT SFARI WGS Non-ASD family AC
+ # SCHEMA schizophrenia case/control (summed across analysis groups)
+ filterByRange.SCHEMAAF_CASE on
+ filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF
+ filterByRange.SCHEMAAF_CTRL on
+ filterLabel.SCHEMAAF_CTRL SCHEMA Control AF
+ filterByRange.SCHEMAAC_CASE on
+ filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC
+ filterByRange.SCHEMAAC_CTRL on
+ filterLabel.SCHEMAAC_CTRL SCHEMA Control AC
+ skipEmptyFields on
+
+ track varFreqsDisease
+ shortLabel Disease-related Databases Combined
+ longLabel Variant Frequencies: Disease-related cohorts combined (autism, schizophrenia, rare disease, NHLBI heart/lung/blood)
+ type bigBed 9 +
+ parent varFreqs off
+ bigDataUrl /gbdb/$D/varFreqs/_disease/varFreqsDisease.bb
+ visibility hide
+ itemRgb on
+ maxWindowToDraw 5000000
+ priority 0.15
+ mouseOver Var: $name
AA change: $aaChange
Var type: $varType
Conseq: $consequence
Max AF: $maxAF
Total AC: $totalAC
Sources: $sources
+ filterValues.sources SPARK|SPARK WES,SFARI_WGS|SFARI WGS,TOPMed|TOPMed,SCHEMA|SCHEMA,GREGoR|GREGoR,GA4K|GA4K PacBio LR
+ filterType.sources multipleListOr
+ filterLabel.sources Source Database
+ 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
+ filterByRange.refLen on
+ filterLabel.refLen Reference Length
+ filterByRange.altLen on
+ filterLabel.altLen Alternate Length
+ filterByRange.varLen on
+ filterLabel.varLen Length Change
+ filterByRange.maxAF on
+ filterLabel.maxAF Max Allele Frequency
+ filterLimits.maxAF 0:1
+ filterByRange.totalAC on
+ filterLabel.totalAC Total Allele Count (all databases)
+ # Per-database AF filters
+ filterByRange.SPARKAF on
+ filterLabel.SPARKAF SPARK WES AF
+ filterByRange.SFARI_WGSAF on
+ filterLabel.SFARI_WGSAF SFARI WGS AF
+ filterByRange.TOPMedAF on
+ filterLabel.TOPMedAF TOPMed AF
+ filterByRange.SCHEMAAF on
+ filterLabel.SCHEMAAF SCHEMA AF
+ filterByRange.GREGoRAF on
+ filterLabel.GREGoRAF GREGoR AF
+ filterByRange.GA4KAF on
+ filterLabel.GA4KAF GA4K PacBio LR AF
+ # Per-database AC filters
+ filterByRange.SPARKAC on
+ filterLabel.SPARKAC SPARK WES AC
+ filterByRange.SFARI_WGSAC on
+ filterLabel.SFARI_WGSAC SFARI WGS AC
+ filterByRange.TOPMedAC on
+ filterLabel.TOPMedAC TOPMed AC
+ filterByRange.SCHEMAAC on
+ filterLabel.SCHEMAAC SCHEMA AC
+ filterByRange.GREGoRAC on
+ filterLabel.GREGoRAC GREGoR AC
+ filterByRange.GA4KAC on
+ filterLabel.GA4KAC GA4K PacBio LR AC
+ # SPARK WES autism phenotype split
+ filterByRange.SPARKAF_AUT on
+ filterLabel.SPARKAF_AUT SPARK WES ASD proband AF
+ filterByRange.SPARKAF_NON_AUT on
+ filterLabel.SPARKAF_NON_AUT SPARK WES Non-ASD family AF
+ filterByRange.SPARKAC_AUT on
+ filterLabel.SPARKAC_AUT SPARK WES ASD proband AC
+ filterByRange.SPARKAC_NON_AUT on
+ filterLabel.SPARKAC_NON_AUT SPARK WES Non-ASD family AC
+ # SFARI WGS autism phenotype split
+ filterByRange.SFARI_WGSAF_AUT on
+ filterLabel.SFARI_WGSAF_AUT SFARI WGS ASD proband AF
+ filterByRange.SFARI_WGSAF_NON_AUT on
+ filterLabel.SFARI_WGSAF_NON_AUT SFARI WGS Non-ASD family AF
+ filterByRange.SFARI_WGSAC_AUT on
+ filterLabel.SFARI_WGSAC_AUT SFARI WGS ASD proband AC
+ filterByRange.SFARI_WGSAC_NON_AUT on
+ filterLabel.SFARI_WGSAC_NON_AUT SFARI WGS Non-ASD family AC
+ # SCHEMA schizophrenia case/control
+ filterByRange.SCHEMAAF_CASE on
+ filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF
+ filterByRange.SCHEMAAF_CTRL on
+ filterLabel.SCHEMAAF_CTRL SCHEMA Control AF
+ filterByRange.SCHEMAAC_CASE on
+ filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC
+ filterByRange.SCHEMAAC_CTRL on
+ filterLabel.SCHEMAAC_CTRL SCHEMA Control AC
+ # GREGoR affected/unaffected/unknown
+ 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 varFreqsArray
+ shortLabel Genotyping Array Databases Combined
+ longLabel Variant Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed)
+ type bigBed 9 +
+ parent varFreqs off
+ bigDataUrl /gbdb/$D/varFreqs/_array/varFreqsArray.bb
+ visibility hide
+ itemRgb on
+ maxWindowToDraw 5000000
+ priority 0.2
+ mouseOver Var: $name
AA change: $aaChange
Var type: $varType
Conseq: $consequence
Max AF: $maxAF
Total AC: $totalAC
Sources: $sources
+ filterValues.sources TPMI|TPMI Taiwan,MexBB|Mexico Biobank,UKBB|UK Biobank imputed
+ filterType.sources multipleListOr
+ filterLabel.sources Source Database
+ filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV
+ filterLabel.varType Variant Type
+ filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other
+ filterType.consequence multipleListOr
+ filterLabel.consequence Consequence
+ filterByRange.refLen on
+ filterLabel.refLen Reference Length
+ filterByRange.altLen on
+ filterLabel.altLen Alternate Length
+ filterByRange.varLen on
+ filterLabel.varLen Length Change
+ filterByRange.maxAF on
+ filterLabel.maxAF Max Allele Frequency
+ filterLimits.maxAF 0:1
+ filterByRange.totalAC on
+ filterLabel.totalAC Total Allele Count (all databases)
+ filterByRange.TPMIAF on
+ filterLabel.TPMIAF TPMI Taiwan AF
+ filterByRange.MexBBAF on
+ filterLabel.MexBBAF Mexico Biobank AF
+ filterByRange.UKBBAF on
+ filterLabel.UKBBAF UK Biobank imputed AF
+ filterByRange.TPMIAC on
+ filterLabel.TPMIAC TPMI Taiwan AC
+ filterByRange.MexBBAC on
+ filterLabel.MexBBAC Mexico Biobank AC
+ filterByRange.UKBBAC on
+ filterLabel.UKBBAC UK Biobank imputed AC
skipEmptyFields on
track allofus
shortLabel AllOfUs v7 245k WGS
longLabel Variant Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_allofus/allOfUs.locAncFreq.vcf.gz
dataVersion V7
visibility hide
tableBrowser off
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
tableBrowser off
visibility hide
priority 2
track sfariSparkExomes
shortLabel SFARI SPARK 140k WES
longLabel Variant Frequencies: SFARI SPARK - 140k WES
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz
dataVersion iWES v3 2024_08
tableBrowser off
visibility hide
priority 2.5
track sfariSparkWgs
shortLabel SFARI SPARK 12k WGS
longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz
dataVersion iWGS v1.1
visibility hide
priority 2.5
html sfariSparkExomes
tableBrowser off
#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 hide
dataVersion 2025-06-16
priority 5
track wbbc
shortLabel China WBBC 4.5k WGS
longLabel Variant Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz
visibility dense
dataVersion Phase I v20210103
priority 5.5
track chinamap
shortLabel China ChinaMAP 10.5k WGS
longLabel Variant Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_chinamap/chinamap.vcf.gz
visibility dense
dataVersion Phase 1 (v2020-03.beta)
priority 5.55
tableBrowser off
track tpmi
shortLabel Taiwan TPMI Axiom array
longLabel Variant Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz
visibility dense
dataVersion Axiom TPM1 2022-06
priority 5.6
tableBrowser off
track alfaVcf
shortLabel NCBI ALFA 408k mixed
longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz
visibility hide
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 hide
type vcfTabix
shortLabel FinnGen R12 500k imputed
longLabel Variant Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS
priority 4.5
bigDataUrl /gbdb/$D/varFreqs/_finngen/finnge_R12_annotated_variants_v1.vcf.gz
dataVersion R12
tableBrowser off
track ukbb
parent varFreqs on
visibility dense
type vcfTabix
shortLabel UK Biobank 361k imputed
longLabel Variant Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed
priority 4.6
bigDataUrl /gbdb/$D/varFreqs/ukbb/ukbb.vcf.gz
dataVersion Neale Lab R2 08-2018
track swefreq
parent varFreqs on
visibility hide
type vcfTabix
shortLabel Sweden SweGen 1k WGS
longLabel Variant Frequencies: Sweden SweGen - 1k WGS
priority 4.7
bigDataUrl /gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz
dataVersion 20251201
tableBrowser off
track gonl
parent varFreqs on
visibility hide
type vcfTabix
shortLabel Netherlands GoNL 498 WGS
longLabel Variant Frequencies: Genome of the Netherlands - 250 Dutch trios
priority 4.75
bigDataUrl /gbdb/$D/varFreqs/gonl/gonl.vcf.gz
dataVersion GRCh38 1.0
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/$D/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz
dataVersion Phase 3
visibility hide
# no downloads as per Matt Hobbs email Jan 28 2026
tableBrowser off
track gasp
shortLabel GenomeAsia 1.7k SNVs
longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz
visibility hide
dataVersion Pilot 2019 (lifted to hg38, May 2026)
track gaspIndel
shortLabel GenomeAsia 1.7k Indels
longLabel Variant Frequencies: GenomeAsia Pilot - Indels
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.indels.vcf.gz
visibility hide
dataVersion Pilot 2019 (lifted to hg38, May 2026)
html gasp
track abraom
shortLabel Brazil ABraOM 1k WGS
longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz
visibility hide
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/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz
visibility hide
dataVersion IndiGen pilot (Jain 2021)
track genomeindia
shortLabel India GenomeIndia 9.7k WGS
longLabel Variant Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025)
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$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/$D/varFreqs/_kova/kova.v7.vcf.gz
visibility hide
tableBrowser off
dataVersion V7
track npm
shortLabel Singapore NPM 9.7k WGS
longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz
visibility hide
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/$D/varFreqs/hrc/hrc.vcf.gz
visibility hide
dataVersion r1.1
track saudi
shortLabel Saudi Genome 302 WGS
longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz
visibility hide
dataVersion SHGP (figshare 51297884, 2025)
track schema
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/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz
visibility hide
dataVersion 2022
priority 4.9
url https://schema.broadinstitute.org/
urlLabel SCHEMA Browser
track mxbFreq
shortLabel Mexico Biobank 6k Array
longLabel Variant Frequencies: Mexico Biobank - 6,011 individuals, genotyping array
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_mxb/mxb.freq.vcf.gz
visibility hide
dataVersion Nov 2025 (hg38 lift)
tableBrowser off
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/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz
visibility hide
dataVersion 2016-12-07 (hg38 lift)
priority 7
track gregor
shortLabel GREGoR R4 3.6k WGS
longLabel Variant Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz
visibility hide
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/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz
visibility hide
dataVersion v3.1.2
priority 8
track ga4kSnv
shortLabel GA4K 552 PacBio LR
longLabel Variant Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz
visibility hide
dataVersion Cohen 2022 release
priority 9
track colorsDbSnv
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/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz
visibility hide
dataVersion v1.2.0
priority 9.5
track svatalogSnv
shortLabel SVatalog 101 WGS
longLabel Variant Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz
visibility hide
dataVersion Chirmade 2025 release
priority 10
track tishkoff180
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 hide
dataVersion Cell 2023 (hg19 lift)
tableBrowser off
priority 7.5