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/scripts/varFreqs/databases.tsv src/hg/makeDb/scripts/varFreqs/databases.tsv index fe84f46d450..fd9cafb6da8 100644 --- src/hg/makeDb/scripts/varFreqs/databases.tsv +++ src/hg/makeDb/scripts/varFreqs/databases.tsv @@ -36,15 +36,16 @@ HRC HRC /gbdb/hg38/varFreqs/hrc/hrc.vcf.gz AC AF 0 # MexBB and TPMI moved to the array-based track (databases_array.tsv): both are # genotyping-array cohorts and are kept out of the WGS/WES varFreqsAll track. SGDP SGDP /gbdb/hg38/varFreqs/sgdpFreq/sgdp.freq.vcf.gz AC AF 0 1 HGDP1kG gnomAD HGDP+1kG /gbdb/hg38/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz AC AF 0 GREGoR GREGoR /gbdb/hg38/varFreqs/gregor/gregor.vcf.gz AC AF 1 SCHEMA SCHEMA /gbdb/hg38/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz AC AF 1 GA4K GA4K PacBio LR /gbdb/hg38/varFreqs/ga4k/ga4kSnv.vcf.gz AC AF 1 affected CoLoRSdb CoLoRSdb PacBio LR /gbdb/hg38/varFreqs/colorsDb/colorsDbSnv.vcf.gz AC AF 0 SVatalog SVatalog 101 10XG SR /gbdb/hg38/varFreqs/svatalog/svatalog.vcf.gz AC AF 0 1 Tishkoff180 Tishkoff 180 African WGS /gbdb/hg38/varFreqs/_tishkoff/tishkoff180.vcf.gz AC AF 0 WBBC WBBC China /gbdb/hg38/varFreqs/wbbc/wbbc.vcf.gz AC AF 0 ChinaMAP China ChinaMAP /gbdb/hg38/varFreqs/_chinamap/chinamap.vcf.gz AC AF 0 GenomeIndia GenomeIndia 9.7k WGS /gbdb/hg38/varFreqs/_genomeindia/genomeindia.vcf.gz AC AF 0 GoNL GoNL Netherlands ~13x SR /gbdb/hg38/varFreqs/gonl/gonl.vcf.gz AC AF 0 +HostSeq HostSeq Canada /gbdb/hg38/varFreqs/hostseq/hostseq.vcf.gz AC AF 0