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/populations.tsv src/hg/makeDb/scripts/varFreqs/populations.tsv index da279c3a887..8598c855df6 100644 --- src/hg/makeDb/scripts/varFreqs/populations.tsv +++ src/hg/makeDb/scripts/varFreqs/populations.tsv @@ -38,15 +38,25 @@ HGDP1kG oth Other gnomad_AC_oth gnomad_AF_oth HGDP1kG sas South Asian gnomad_AC_sas gnomad_AF_sas # GREGoR affected/unaffected breakdown GREGoR AFF Affected AC_AFFECTED . affected GREGoR UNA Unaffected AC_UNAFFECTED . unaffected GREGoR UNK Unknown AC_UNKNOWN . unknown # NPM Singapore (SG10K_Health) ancestry groups NPM Chinese Singapore Chinese AC_SgChinese AF_SgChinese NPM Malay Singapore Malay AC_SgMalay AF_SgMalay NPM Indian Singapore Indian AC_SgIndian AF_SgIndian # WBBC Westlake BioBank for Chinese regional Han groups (AC not present, will be synthesized from AF*AN at build time) WBBC North North Han . North_AF WBBC Central Central Han . Central_AF WBBC South South Han . South_AF WBBC Lingnan Lingnan Han . Lingnan_AF +# gnomAD-Canada HostSeq genetic-ancestry groups (key "oth" = Remaining/Other) +HostSeq afr African/African-American AC_afr AF_afr +HostSeq amr Latino/Admixed-American AC_amr AF_amr +HostSeq asj Ashkenazi Jewish AC_asj AF_asj +HostSeq eas East Asian AC_eas AF_eas +HostSeq fin European (Finnish) AC_fin AF_fin +HostSeq mid Middle Eastern AC_mid AF_mid +HostSeq nfe European (non-Finnish) AC_nfe AF_nfe +HostSeq oth Remaining/Other AC_oth AF_oth +HostSeq sas South Asian AC_sas AF_sas