d5302bd1e0cf296545df9ad3e0d3ab57859a51eb lrnassar Fri Jul 24 17:17:17 2026 -0700 varFreqs: post-QA polish on new hostseq subtrack. refs #37882 Findings from the qa-track pass on the gnomAD-Canada HostSeq subtrack added in 99764ad55bb: - hostseq.html: fix non-ASCII byte in Alföldi (Alföldi), swap hardcoded hg38 for $db in the hgdownload URL, extend the FILTER enumeration to include InbreedingCoeff;RF (34,540 sites), add nhomalt and grpmax to the Display Conventions details-page list, and add an "Effective sample size per ancestry group" subsection warning that AF_fin (~4 individuals) and AF_mid (~72) are too sparse to be reliable population estimates. Collapsed a stray double blank line between refs. - populations.tsv, hostseqHtToVcf.py: harmonize the "oth" group label to "Remaining individuals" per the gnomAD README. The existing VCF header still shows the old label; it picks up the new one on the next re-emit (not worth re-running the 104 GB Hail table just for this). - varFreqs.ra: hostseq priority 2 -> 33 to break the sort-order collision with allofus (also at priority 2). diff --git src/hg/makeDb/scripts/varFreqs/populations.tsv src/hg/makeDb/scripts/varFreqs/populations.tsv index 8598c855df6..6c8bfd17b01 100644 --- src/hg/makeDb/scripts/varFreqs/populations.tsv +++ src/hg/makeDb/scripts/varFreqs/populations.tsv @@ -38,25 +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) +# gnomAD-Canada HostSeq genetic-ancestry groups (key "oth" = Remaining individuals) 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 oth Remaining individuals AC_oth AF_oth HostSeq sas South Asian AC_sas AF_sas