f0d9b9d7a69a43e62c52d80b18ef06ba1bf335ed
lrnassar
Fri Jun 12 02:40:53 2026 -0700
varFreqs: add "tableBrowser off" to every subtrack whose bigDataUrl points
into an underscore-prefixed /gbdb dir (the rsync-exclusion convention for
non-redistributable cohorts). Covers varFreqsAffected, varFreqsBackground,
varFreqsArray, and genomeindia which were missing it.
Also fix the "Downloadable from UCSC" column on the supertrack page for
TOPMed, FinnGen and GenomeIndia (table said "Yes" but their gbdb paths
are underscore-prefixed, so they aren't actually downloadable from us).
refs #36642
diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra
index 7e8a3c3d634..865e6164400 100644
--- src/hg/makeDb/trackDb/human/varFreqs.ra
+++ src/hg/makeDb/trackDb/human/varFreqs.ra
@@ -1,29 +1,30 @@
track varFreqs
shortLabel SNV Frequencies
longLabel SNV Frequencies from various cohorts or national projects
group varRep
type bed 12
visibility hide
superTrack on
track varFreqsAffected
shortLabel Disease cohorts
longLabel SNV Frequencies: variants in ~130,000 affected or case individuals (autism, schizophrenia, rare disease cohorts)
type bigBed 9 +
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_affected/varFreqsAffected.bb
+ tableBrowser off
visibility pack
itemRgb on
maxWindowToDraw 5000000
priority 0.11
mouseOver Var: ${name}
AA change: ${aaChange}
Var type: ${varType}
Conseq: ${consequence}
Affected AF: ${affectedAF}
Affected AC/AN: ${affectedAC} / ${affectedAN}
Affected cohorts: ${affectedCohorts}
Background AF: ${backgroundAF}
filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR
filterType.affectedCohorts multipleListOr
filterLabel.affectedCohorts Affected/case cohort
filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR
filterType.backgroundSources multipleListOr
filterLabel.backgroundSources Background source (population or unaffected)
# Variant type and consequence filters
filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV
filterLabel.varType Variant Type
filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other
@@ -339,30 +340,31 @@
filterLabel.WBBCAC_North WBBC China North Han AC
filterByRange.WBBCAC_Central on
filterLabel.WBBCAC_Central WBBC China Central Han AC
filterByRange.WBBCAC_South on
filterLabel.WBBCAC_South WBBC China South Han AC
filterByRange.WBBCAC_Lingnan on
filterLabel.WBBCAC_Lingnan WBBC China Lingnan Han AC
skipEmptyFields on
track varFreqsBackground
shortLabel Population reference
longLabel SNV Frequencies: variants in ~1.5 million individuals from population cohorts and unaffected or control arms
type bigBed 9 +
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_background/varFreqsBackground.bb
+ tableBrowser off
visibility pack
itemRgb on
maxWindowToDraw 5000000
priority 0.1
mouseOver Var: ${name}
AA change: ${aaChange}
Var type: ${varType}
Conseq: ${consequence}
Background AF: ${backgroundAF}
Background AC/AN: ${backgroundAC} / ${backgroundAN}
Sources: ${backgroundSources}
Affected AF: ${affectedAF}
filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR
filterType.affectedCohorts multipleListOr
filterLabel.affectedCohorts Affected/case cohort
filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR
filterType.backgroundSources multipleListOr
filterLabel.backgroundSources Background source (population or unaffected)
# Variant type and consequence filters
filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV
filterLabel.varType Variant Type
filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other
@@ -678,30 +680,31 @@
filterLabel.WBBCAC_North WBBC China North Han AC
filterByRange.WBBCAC_Central on
filterLabel.WBBCAC_Central WBBC China Central Han AC
filterByRange.WBBCAC_South on
filterLabel.WBBCAC_South WBBC China South Han AC
filterByRange.WBBCAC_Lingnan on
filterLabel.WBBCAC_Lingnan WBBC China Lingnan Han AC
skipEmptyFields on
track varFreqsArray
shortLabel Genotyping Array Databases Combined
longLabel SNV Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed)
type bigBed 9 +
parent varFreqs off
bigDataUrl /gbdb/$D/varFreqs/_array/varFreqsArray.bb
+ tableBrowser off
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: $sources
filterValues.sources TPMI|TPMI Taiwan,MexBB|Mexico Biobank,UKBB|UK Biobank imputed
filterType.sources multipleListOr
filterLabel.sources Source Database
filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV
filterLabel.varType Variant Type
filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other
filterType.consequence multipleListOr
filterLabel.consequence Consequence
filterByRange.refLen on
filterLabel.refLen Reference Length
@@ -934,30 +937,31 @@
track indigenomes
shortLabel India IndiGenomes 1k WGS
longLabel SNV Frequencies: IndiGenomes India - 1,029 samples
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz
visibility hide
dataVersion IndiGen pilot (Jain 2021)
track genomeindia
shortLabel India GenomeIndia 9.7k WGS
longLabel SNV Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025)
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_genomeindia/genomeindia.vcf.gz
+ tableBrowser off
visibility hide
dataVersion 9768GI_SummaryStats (Apr 2025)
priority 4.8
track kova
shortLabel Korea KOVA 5.3k mixed
longLabel SNV Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES
type vcfTabix
parent varFreqs on
bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz
visibility hide
tableBrowser off
dataVersion V7
track npm