442e433a90b25deb87f10e6cf1b7b608bb0a6d67 max Sat Sep 26 21:56:06 2026 -0700 sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 8dcc03a5022..05ffd81c3c3 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -7,34 +7,34 @@ superTrack on pennantIcon New red ../goldenPath/newsarch.html#070126 "Released Jul. 1, 2026" 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}
Top affected by AF: ${topAffectedSources}
Background AF: ${backgroundAF} - filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR + filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK iWGS v1.1 Pilot,SPARK45k|SFARI SPARK 45k 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,HostSeq|HostSeq Canada + filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK iWGS v1.1 Pilot,SPARK45k|SFARI SPARK 45k 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,HostSeq|HostSeq Canada 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 filterType.consequence multipleListOr filterLabel.consequence Consequence # Length filters filterByRange.refLen on filterLabel.refLen Reference Length filter.refLen 1:28037 filterLimits.refLen 1:28037 filterByRange.altLen on filterLabel.altLen Alternate Length @@ -633,34 +633,34 @@ # filterLimits.WBBCAC_Lingnan 0:2000000 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}
Top population sources by AF: ${topBackgroundSources}
Affected AF: ${affectedAF} - filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR + filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK iWGS v1.1 Pilot,SPARK45k|SFARI SPARK 45k 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,HostSeq|HostSeq Canada + filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK iWGS v1.1 Pilot,SPARK45k|SFARI SPARK 45k 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,HostSeq|HostSeq Canada 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 filterType.consequence multipleListOr filterLabel.consequence Consequence # Length filters filterByRange.refLen on filterLabel.refLen Reference Length filter.refLen 1:28037 filterLimits.refLen 1:28037 filterByRange.altLen on filterLabel.altLen Alternate Length @@ -1358,30 +1358,31 @@ dataVersion iWGS v1.1 visibility hide priority 25 html sfariSparkExomes tableBrowser off track sfariSparkWgs45kAsd shortLabel SFARI SPARK 45k WGS ASD longLabel SNV Frequencies: SFARI SPARK - 45,178 WGS, August 2026 release, from genotypes, ASD/non-ASD counts type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/sparkWgs45kAsd.vcf.gz dataVersion SPARK WGS 2026_08 visibility hide priority 24.1 + excludeFilterValues NonHumanIns html sfariSparkExomes tableBrowser off filter.AF 0:1 filterByRange.AF on filterLimits.AF 0:1 filterLabel.AF Allele frequency, all filter.AF_AUT 0:1 filterByRange.AF_AUT on filterLimits.AF_AUT 0:1 filterLabel.AF_AUT Allele frequency, autistic filter.AF_NON_AUT 0:1 filterByRange.AF_NON_AUT on filterLimits.AF_NON_AUT 0:1 filterLabel.AF_NON_AUT Allele frequency, non-autistic filter.VARLEN -400:1100