5ad55adbb6a5cc72a393700130584aa87fef2c89 lrnassar Tue Jun 30 06:15:44 2026 -0700 varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642 Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the three cohorts/arms with the highest per-source AF, formatted as "Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population cohorts use the bare key. Per-population sub-ancestries are deliberately excluded so a high sub-pop AF cannot crowd out actual project-level signals. vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into affected_arm_afs / background_arm_afs, and emits two new fields topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165. An AF-distribution sweep across all 28 source cohorts identified SGDP and SVatalog as encoding allele counts per genotyped individual (small N, AF defaults near 0.5), making their per-source AF unreliable for the ranking. Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still appear in backgroundSources; they are only suppressed from the Top 3. Description pages varFreqsAffected.html and varFreqsBackground.html document the ranking; the latter also documents the SGDP/SVatalog exclusion. Build documentation in varFreqs.txt is updated. diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index f056f6c92b0..bd38b65f641 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -6,31 +6,31 @@ visibility hide superTrack on pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD" 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} + 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: ${backgroundAF} filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR filterType.affectedCohorts multipleListOr filterLabel.affectedCohorts Affected/case cohort filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR filterType.backgroundSources multipleListOr filterLabel.backgroundSources Background source (population or unaffected) # Variant type and consequence filters filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence # Length filters filterByRange.refLen on filterLabel.refLen Reference Length @@ -624,31 +624,31 @@ # filter.WBBCAC_Lingnan 0:2000000 # filterLimits.WBBCAC_Lingnan 0:2000000 skipEmptyFields on track varFreqsBackground shortLabel Population reference longLabel SNV Frequencies: variants in ~1.5 million individuals from population cohorts and unaffected or control arms type bigBed 9 + parent varFreqs on bigDataUrl /gbdb/$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}
Affected AF: ${affectedAF} + 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 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 filterType.consequence multipleListOr filterLabel.consequence Consequence # Length filters filterByRange.refLen on filterLabel.refLen Reference Length