99764ad55bb121d285e9734de955bba41802ad06 max Wed Jul 15 23:35:19 2026 -0700 varFreqs: add gnomAD-Canada HostSeq SNV frequencies and fold into combined tracks, refs #36642 #Preview2 week - bugs introduced now will need a build patch to fix New "hostseq" vcfTabix subtrack of the SNV Frequencies container: gnomAD-Canada v1.0 / HostSeq, 10,487 Canadian COVID-19 WGS genomes on hg38. The release ships only as a ~104 GB Hail table, so hostseqHtToVcf.py reads it with Hail and flattens the freq array into a sites-only VCF with overall + 9 gnomAD ancestry-group AC/AN/AF, nhomalt, grpmax, dbSNP rsID and the variant filter status. 232,028,491 release rows -> 213,382,086 written (18,646,405 AC0 sites dropped). Registered HostSeq (is_disease=0) in databases.tsv and its 9 ancestry groups in populations.tsv, and rebuilt varFreqsAffected/varFreqsBackground so HostSeq feeds the background side (29 cohorts, 185 fields; merged set 1,374,129,993 variants). Added HostSeq to filterValues.backgroundSources. diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index c9d117642e9..62b6832f96e 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -10,31 +10,31 @@ 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 <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>Top affected by AF:</b> ${topAffectedSources}<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 + 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 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 @@ -176,30 +176,34 @@ # filterLabel.WBBCAF WBBC China AF # filter.WBBCAF 0:1 # filterLimits.WBBCAF 0:1 # filterByRange.ChinaMAPAF on # filterLabel.ChinaMAPAF China ChinaMAP AF # filter.ChinaMAPAF 0:1 # filterLimits.ChinaMAPAF 0:1 # filterByRange.GenomeIndiaAF on # filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF # filter.GenomeIndiaAF 0:1 # filterLimits.GenomeIndiaAF 0:1 # filterByRange.GoNLAF on # filterLabel.GoNLAF GoNL Netherlands ~13x SR AF # filter.GoNLAF 0:1 # filterLimits.GoNLAF 0:1 + # filterByRange.HostSeqAF on + # filterLabel.HostSeqAF HostSeq Canada AF + # filter.HostSeqAF 0:1 + # filterLimits.HostSeqAF 0:1 # Per-database AC filters (commented out: re-enable as needed) # filterByRange.AllOfUsAC on # filterLabel.AllOfUsAC AllOfUs AC # filter.AllOfUsAC 0:2000000 # filterLimits.AllOfUsAC 0:2000000 # filterByRange.SPARKAC on # filterLabel.SPARKAC SFARI SPARK WES AC # filter.SPARKAC 0:2000000 # filterLimits.SPARKAC 0:2000000 # filterByRange.SFARI_WGSAC on # filterLabel.SFARI_WGSAC SFARI SPARK WGS AC # filter.SFARI_WGSAC 0:2000000 # filterLimits.SFARI_WGSAC 0:2000000 # filterByRange.GenomeAsiaAC on # filterLabel.GenomeAsiaAC GenomeAsia SNVs AC @@ -289,30 +293,34 @@ # filterLabel.WBBCAC WBBC China AC # filter.WBBCAC 0:2000000 # filterLimits.WBBCAC 0:2000000 # filterByRange.ChinaMAPAC on # filterLabel.ChinaMAPAC China ChinaMAP AC # filter.ChinaMAPAC 0:2000000 # filterLimits.ChinaMAPAC 0:2000000 # filterByRange.GenomeIndiaAC on # filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC # filter.GenomeIndiaAC 0:2000000 # filterLimits.GenomeIndiaAC 0:2000000 # filterByRange.GoNLAC on # filterLabel.GoNLAC GoNL Netherlands ~13x SR AC # filter.GoNLAC 0:2000000 # filterLimits.GoNLAC 0:2000000 + # filterByRange.HostSeqAC on + # filterLabel.HostSeqAC HostSeq Canada AC + # filter.HostSeqAC 0:2000000 + # filterLimits.HostSeqAC 0:2000000 # Population-specific AF/AC filters (commented out: re-enable as needed) # AllOfUs populations # filterByRange.AllOfUsAF_AFR on # filterLabel.AllOfUsAF_AFR AllOfUs African AF # filter.AllOfUsAF_AFR 0:1 # filterLimits.AllOfUsAF_AFR 0:1 # filterByRange.AllOfUsAF_AMR on # filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF # filter.AllOfUsAF_AMR 0:1 # filterLimits.AllOfUsAF_AMR 0:1 # filterByRange.AllOfUsAF_EAS on # filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF # filter.AllOfUsAF_EAS 0:1 # filterLimits.AllOfUsAF_EAS 0:1 # filterByRange.AllOfUsAF_EUR on @@ -628,31 +636,31 @@ 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 <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>Top population sources by AF:</b> ${topBackgroundSources}<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 + 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 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 @@ -794,30 +802,34 @@ # filterLabel.WBBCAF WBBC China AF # filter.WBBCAF 0:1 # filterLimits.WBBCAF 0:1 # filterByRange.ChinaMAPAF on # filterLabel.ChinaMAPAF China ChinaMAP AF # filter.ChinaMAPAF 0:1 # filterLimits.ChinaMAPAF 0:1 # filterByRange.GenomeIndiaAF on # filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF # filter.GenomeIndiaAF 0:1 # filterLimits.GenomeIndiaAF 0:1 # filterByRange.GoNLAF on # filterLabel.GoNLAF GoNL Netherlands ~13x SR AF # filter.GoNLAF 0:1 # filterLimits.GoNLAF 0:1 + # filterByRange.HostSeqAF on + # filterLabel.HostSeqAF HostSeq Canada AF + # filter.HostSeqAF 0:1 + # filterLimits.HostSeqAF 0:1 # Per-database AC filters (commented out: re-enable as needed) # filterByRange.AllOfUsAC on # filterLabel.AllOfUsAC AllOfUs AC # filter.AllOfUsAC 0:2000000 # filterLimits.AllOfUsAC 0:2000000 # filterByRange.SPARKAC on # filterLabel.SPARKAC SFARI SPARK WES AC # filter.SPARKAC 0:2000000 # filterLimits.SPARKAC 0:2000000 # filterByRange.SFARI_WGSAC on # filterLabel.SFARI_WGSAC SFARI SPARK WGS AC # filter.SFARI_WGSAC 0:2000000 # filterLimits.SFARI_WGSAC 0:2000000 # filterByRange.GenomeAsiaAC on # filterLabel.GenomeAsiaAC GenomeAsia SNVs AC @@ -907,30 +919,34 @@ # filterLabel.WBBCAC WBBC China AC # filter.WBBCAC 0:2000000 # filterLimits.WBBCAC 0:2000000 # filterByRange.ChinaMAPAC on # filterLabel.ChinaMAPAC China ChinaMAP AC # filter.ChinaMAPAC 0:2000000 # filterLimits.ChinaMAPAC 0:2000000 # filterByRange.GenomeIndiaAC on # filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC # filter.GenomeIndiaAC 0:2000000 # filterLimits.GenomeIndiaAC 0:2000000 # filterByRange.GoNLAC on # filterLabel.GoNLAC GoNL Netherlands ~13x SR AC # filter.GoNLAC 0:2000000 # filterLimits.GoNLAC 0:2000000 + # filterByRange.HostSeqAC on + # filterLabel.HostSeqAC HostSeq Canada AC + # filter.HostSeqAC 0:2000000 + # filterLimits.HostSeqAC 0:2000000 # Population-specific AF/AC filters (commented out: re-enable as needed) # AllOfUs populations # filterByRange.AllOfUsAF_AFR on # filterLabel.AllOfUsAF_AFR AllOfUs African AF # filter.AllOfUsAF_AFR 0:1 # filterLimits.AllOfUsAF_AFR 0:1 # filterByRange.AllOfUsAF_AMR on # filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF # filter.AllOfUsAF_AMR 0:1 # filterLimits.AllOfUsAF_AMR 0:1 # filterByRange.AllOfUsAF_EAS on # filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF # filter.AllOfUsAF_EAS 0:1 # filterLimits.AllOfUsAF_EAS 0:1 # filterByRange.AllOfUsAF_EUR on @@ -1640,15 +1656,25 @@ visibility hide dataVersion Chirmade 2025 release priority 29 track tishkoff180 shortLabel 12 Afr Pops 180 WGS longLabel SNV Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tishkoff/tishkoff180.vcf.gz visibility hide dataVersion Cell 2023 (hg19 lift) tableBrowser off priority 1 + track hostseq + shortLabel Canada HostSeq 10.5k WGS + longLabel SNV Frequencies: gnomAD-Canada HostSeq - 10,487 WGS, Canadian COVID-19 cohort + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/hostseq/hostseq.vcf.gz + visibility hide + dataVersion gnomAD-Canada v1.0 + priority 2 +