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