5c88f2b10f443d95e3f9c8e4bbc81534b78d9222 max Thu May 21 00:40:38 2026 -0700 varFreqs: rename supertrack to "SNV Frequencies"; add GoNL (Netherlands, ~13x SR) to databases.tsv and to the varFreqsAll filter UI so the next combined-track rebuild picks it up. refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index cc57ab88606..1c43df781e0 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,36 +1,36 @@ track varFreqs -shortLabel Variant Frequencies -longLabel Variant Frequencies from various cohorts or national projects +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 <b>Var:</b> $name<br><b>AA change:</b> $aaChange<br><b>Var type:</b> $varType<br><b>Conseq:</b> $consequence<br><b>Max AF:</b> $maxAF<br><b>Total AC:</b> $totalAC<br><b>Sources:</b> $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 + 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 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 @@ -88,30 +88,32 @@ 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 @@ -147,30 +149,32 @@ 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