6b285a53b036b309e3c7a9b61d3741731088a172 lrnassar Fri Jun 12 02:35:01 2026 -0700 varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled sum(AC)/sum(AN) so the rate matches the carrier count scale. Per-arm AN is derived as round(AC/AF) when both are reported. An optional "default_an" column was added to databases.tsv so AF-only cohorts (ABraOM, ALFA) can synthesize a denominator from their cohort size; without it those cohorts had been silently dropped from the pooled rate. New affectedAN and backgroundAN columns expose the pool denominator. The mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is visible. Per-arm cohorts that ship only AC and no default_an (MGRB, GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still listed in affectedCohorts/backgroundSources but contribute 0 to the pool, preserving the invariant pool_AF <= 1. The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected against the existing merged.annotated.vcf.gz. refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 8bf3d890953..7e8a3c3d634 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -4,68 +4,72 @@ 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 visibility pack itemRgb on maxWindowToDraw 5000000 priority 0.11 - mouseOver <b>Var:</b> ${name}<br><b>AA change:</b> ${aaChange}<br><b>Var type:</b> ${varType}<br><b>Conseq:</b> ${consequence}<br><b>Affected AF:</b> ${affectedAF}<br><b>Affected AC:</b> ${affectedAC}<br><b>Affected cohorts:</b> ${affectedCohorts}<br><b>Background AF:</b> ${backgroundAF} + mouseOver <b>Var:</b> ${name}<br><b>AA change:</b> ${aaChange}<br><b>Var type:</b> ${varType}<br><b>Conseq:</b> ${consequence}<br><b>Affected AF:</b> ${affectedAF}<br><b>Affected AC/AN:</b> ${affectedAC} / ${affectedAN}<br><b>Affected cohorts:</b> ${affectedCohorts}<br><b>Background AF:</b> ${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 filter.refLen 1:28037 filterLimits.refLen 1:28037 filterByRange.altLen on filterLabel.altLen Alternate Length filter.altLen 1:6294 filterLimits.altLen 1:6294 filterByRange.varLen on filterLabel.varLen Length Change filter.varLen -28036:6293 filterLimits.varLen -28036:6293 # Affected/case frequency summary filterByRange.affectedAF on - filterLabel.affectedAF Affected/case AF + filterLabel.affectedAF Affected/case AF (pooled) filterLimits.affectedAF 0:1 filterByRange.affectedAC on filterLabel.affectedAC Affected/case AC + filterByRange.affectedAN on + filterLabel.affectedAN Affected/case AN (pool denominator) # Background (population + unaffected) frequency summary filterByRange.backgroundAF on - filterLabel.backgroundAF Background AF (population + unaffected) + filterLabel.backgroundAF Background AF (pooled) filterLimits.backgroundAF 0:1 filterByRange.backgroundAC on filterLabel.backgroundAC Background AC (population + unaffected) + filterByRange.backgroundAN on + filterLabel.backgroundAN Background AN (pool denominator) # Affected/case membership flag filterByRange.inAffected on filterLabel.inAffected Seen in an affected/case arm (1=yes, 0=no) filter.inAffected 0:1 filterLimits.inAffected 0:1 # Per-database AF filters filterByRange.AllOfUsAF on filterLabel.AllOfUsAF AllOfUs AF filterByRange.SPARKAF on filterLabel.SPARKAF SFARI SPARK WES AF filterByRange.SFARI_WGSAF on filterLabel.SFARI_WGSAF SFARI SPARK WGS AF filterByRange.GenomeAsiaAF on filterLabel.GenomeAsiaAF GenomeAsia SNVs AF filterByRange.GenomeAsiaIndelAF on @@ -339,68 +343,72 @@ 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 visibility pack itemRgb on maxWindowToDraw 5000000 priority 0.1 - mouseOver <b>Var:</b> ${name}<br><b>AA change:</b> ${aaChange}<br><b>Var type:</b> ${varType}<br><b>Conseq:</b> ${consequence}<br><b>Background AF:</b> ${backgroundAF}<br><b>Background AC:</b> ${backgroundAC}<br><b>Sources:</b> ${backgroundSources}<br><b>Affected AF:</b> ${affectedAF} + mouseOver <b>Var:</b> ${name}<br><b>AA change:</b> ${aaChange}<br><b>Var type:</b> ${varType}<br><b>Conseq:</b> ${consequence}<br><b>Background AF:</b> ${backgroundAF}<br><b>Background AC/AN:</b> ${backgroundAC} / ${backgroundAN}<br><b>Sources:</b> ${backgroundSources}<br><b>Affected AF:</b> ${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 filter.refLen 1:28037 filterLimits.refLen 1:28037 filterByRange.altLen on filterLabel.altLen Alternate Length filter.altLen 1:6294 filterLimits.altLen 1:6294 filterByRange.varLen on filterLabel.varLen Length Change filter.varLen -28036:6293 filterLimits.varLen -28036:6293 # Affected/case frequency summary filterByRange.affectedAF on - filterLabel.affectedAF Affected/case AF + filterLabel.affectedAF Affected/case AF (pooled) filterLimits.affectedAF 0:1 filterByRange.affectedAC on filterLabel.affectedAC Affected/case AC + filterByRange.affectedAN on + filterLabel.affectedAN Affected/case AN (pool denominator) # Background (population + unaffected) frequency summary filterByRange.backgroundAF on - filterLabel.backgroundAF Background AF (population + unaffected) + filterLabel.backgroundAF Background AF (pooled) filterLimits.backgroundAF 0:1 filterByRange.backgroundAC on filterLabel.backgroundAC Background AC (population + unaffected) + filterByRange.backgroundAN on + filterLabel.backgroundAN Background AN (pool denominator) # Affected/case membership flag filterByRange.inAffected on filterLabel.inAffected Seen in an affected/case arm (1=yes, 0=no) filter.inAffected 0:1 filterLimits.inAffected 0:1 # Per-database AF filters filterByRange.AllOfUsAF on filterLabel.AllOfUsAF AllOfUs AF filterByRange.SPARKAF on filterLabel.SPARKAF SFARI SPARK WES AF filterByRange.SFARI_WGSAF on filterLabel.SFARI_WGSAF SFARI SPARK WGS AF filterByRange.GenomeAsiaAF on filterLabel.GenomeAsiaAF GenomeAsia SNVs AF filterByRange.GenomeAsiaIndelAF on