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 @@ -1,52 +1,62 @@ # Population breakdown configuration for varFreqsAll combined track # db_key pop_key pop_name ac_field af_field [phenotype] # Optional 6th column "phenotype" (affected|unaffected|unknown) tags a disease cohort's # case/control arms so the build can aggregate an affected-vs-unaffected summary across # cohorts. Ancestry/region populations leave it blank. # AllOfUs local ancestry populations AllOfUs AFR African AC_AFR AF_AFR AllOfUs AMR Indigenous American AC_AMR AF_AMR AllOfUs EAS East Asian AC_EAS AF_EAS AllOfUs EUR European AC_EUR AF_EUR AllOfUs OCE Oceanian AC_OCE AF_OCE AllOfUs SAS South Asian AC_SAS AF_SAS # SFARI SPARK autism phenotype split (asd column of individuals_registration) SPARK AUT ASD proband AC_AUT AF_AUT affected SPARK NON_AUT Non-ASD family AC_NON_AUT AF_NON_AUT unaffected SFARI_WGS AUT ASD proband AC_AUT AF_AUT affected SFARI_WGS NON_AUT Non-ASD family AC_NON_AUT AF_NON_AUT unaffected # SCHEMA schizophrenia case/control split (summed across analysis groups) SCHEMA CASE Schizophrenia case AC_CASE AF_CASE affected SCHEMA CTRL Control AC_CTRL AF_CTRL unaffected # GenomeAsia populations (7 groups in source VCF) GenomeAsia NEA Northeast Asian AC_NEA AF_NEA GenomeAsia SEA Southeast Asian AC_SEA AF_SEA GenomeAsia SAS South Asian AC_SAS AF_SAS GenomeAsia OCE Oceanian AC_OCE AF_OCE GenomeAsia AMR American AC_AMR AF_AMR GenomeAsia AFR African AC_AFR AF_AFR GenomeAsia WER Western European Ref AC_WER AF_WER # gnomAD HGDP+1kG continental groups HGDP1kG afr African gnomad_AC_afr gnomad_AF_afr HGDP1kG ami Amish gnomad_AC_ami gnomad_AF_ami HGDP1kG amr Latino gnomad_AC_amr gnomad_AF_amr HGDP1kG asj Ashkenazi Jewish gnomad_AC_asj gnomad_AF_asj HGDP1kG eas East Asian gnomad_AC_eas gnomad_AF_eas HGDP1kG fin Finnish gnomad_AC_fin gnomad_AF_fin HGDP1kG mid Middle Eastern gnomad_AC_mid gnomad_AF_mid HGDP1kG nfe Non-Finnish European gnomad_AC_nfe gnomad_AF_nfe 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