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/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra
index 62b6832f96e..3b8fc94e206 100644
--- src/hg/makeDb/trackDb/human/varFreqs.ra
+++ src/hg/makeDb/trackDb/human/varFreqs.ra
@@ -1664,17 +1664,17 @@
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/_tishkoff/tishkoff180.vcf.gz
         visibility hide
         dataVersion Cell 2023 (hg19 lift)
         tableBrowser off
         priority 1
 
         track hostseq
         shortLabel Canada HostSeq 10.5k WGS
         longLabel SNV Frequencies: gnomAD-Canada HostSeq - 10,487 WGS, Canadian COVID-19 cohort
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/hostseq/hostseq.vcf.gz
         visibility hide
         dataVersion gnomAD-Canada v1.0
-        priority 2
+        priority 33