86744c40b7e7f18792d287aedf9cf5da543e2d5a
max
  Fri Apr 17 07:22:27 2026 -0700
Add GA4K (Genomic Answers for Kids) small-variant subtrack to the
Variant Frequencies supertrack for hg38.
#Preview2 week - bugs introduced now will need a build patch to fix

Children's Mercy pediatric rare-disease cohort: ~36.2M SNVs and short
indels from 552 PacBio HiFi long-read samples (DeepVariant/GLnexus),
filtered to variants replicated in >=2 unrelated GA4K individuals or
an HPRC variant. Ref: Cohen et al. 2022, Genet Med, PMID 35305867.

refs #36642

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra
index 0f7a4cdbe9c..b2a2c5fe5da 100644
--- src/hg/makeDb/trackDb/human/varFreqs.ra
+++ src/hg/makeDb/trackDb/human/varFreqs.ra
@@ -451,15 +451,24 @@
         bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz
         visibility pack
         dataVersion R04 (Oct 2025)
         priority 8
 
         track hgdp1kFreq
         shortLabel gnomAD HGDP+1kG 4k WGS
         longLabel Variant Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz
         visibility pack
         dataVersion v3.1.2
         priority 8
 
+        track ga4kSnv
+        shortLabel GA4K 552 PacBio LR
+        longLabel Variant Frequencies: Genomic Answers for Kids (Children's Mercy) - 552 PacBio HiFi long-read WGS (pediatric rare-disease cohort)
+        type vcfTabix
+        parent varFreqs on
+        bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz
+        visibility pack
+        priority 9
+