e89a2c6a10b38da2591e8e4e7132fe29a4b1fbd7
max
  Mon Apr 20 09:31:08 2026 -0700
varFreqs: add colorsDbSnv subtrack (hg38 and hs1)

CoLoRSdb v1.2.0 long-read SNV/indel population-frequency VCFs from 1,027
PacBio HiFi whole genomes, joint-called with DeepVariant and GLnexus.
The GRCh38 release is shown on hg38 and the CHM13 release on hs1 (both
are native, not lifted). This is the first varFreqs subtrack that
renders on hs1.

refs #36642

diff --git src/hg/makeDb/doc/hg38/varFreqs.txt src/hg/makeDb/doc/hg38/varFreqs.txt
index 3051e5f2e12..0dcc1232735 100644
--- src/hg/makeDb/doc/hg38/varFreqs.txt
+++ src/hg/makeDb/doc/hg38/varFreqs.txt
@@ -227,15 +227,38 @@
 # Received from Qudsi at UCSC in the Ioannidis group via phoenix
 # only concated and ran tabix on it
 cd /hive/data/genomes/hg38/bed/varFreqs/allofus/
 bcftools concat --threads 16 -Oz -o allOfUs.locAncFreq.vcf.gz clean/allele_freq_chr{1..22}.NW.clean.conf90.oneline.vcf.gz
 tabix allOfUs.locAncFreq.vcf.gz
 
 ##########
 # 2026-03-27 Claude max
 
 # Two phased SV VCF tracks moved into phasedVars superTrack from lrSv:
 # - han945SvVcf: Per-sample genotypes for 945 Han Chinese SVs
 # - lrSv1kgOntPhased: Phased SVs from 1,019 diverse humans (1KG ONT)
 # Data files remain in /hive/data/genomes/hg38/bed/lrSv/
 # Symlinks moved from /gbdb/{hg38,hs1}/lrSv/ to /gbdb/{hg38,hs1}/phasedVars/
 # Build documentation for these tracks is in lrSv.txt
+
+##########
+# 2026-04-20 Claude max
+
+# CoLoRSdb v1.2.0 long-read SNV/indel population frequencies added as
+# the colorsDbSnv subtrack of varFreqs, for both hg38 and hs1.
+#
+# Upstream VCFs (GRCh38 and CHM13 releases) are already present in
+# /hive/data/genomes/hg38/bed/lrSv/colorsDb/ (placed there when the
+# CoLoRSdb SV track was first built under lrSv). We just add VCF
+# symlinks under each assembly's varFreqs directory using a consistent
+# filename so the shared trackDb stanza can use $D.
+
+mkdir -p /gbdb/hg38/varFreqs/colorsDb /gbdb/hs1/varFreqs/colorsDb
+ln -sf /hive/data/genomes/hg38/bed/lrSv/colorsDb/CoLoRSdb.GRCh38.v1.2.0.deepvariant.glnexus.vcf.gz     /gbdb/hg38/varFreqs/colorsDb/colorsDbSnv.vcf.gz
+ln -sf /hive/data/genomes/hg38/bed/lrSv/colorsDb/CoLoRSdb.GRCh38.v1.2.0.deepvariant.glnexus.vcf.gz.tbi /gbdb/hg38/varFreqs/colorsDb/colorsDbSnv.vcf.gz.tbi
+ln -sf /hive/data/genomes/hg38/bed/lrSv/colorsDb/CoLoRSdb.CHM13.v1.2.0.deepvariant.glnexus.vcf.gz      /gbdb/hs1/varFreqs/colorsDb/colorsDbSnv.vcf.gz
+ln -sf /hive/data/genomes/hg38/bed/lrSv/colorsDb/CoLoRSdb.CHM13.v1.2.0.deepvariant.glnexus.vcf.gz.tbi  /gbdb/hs1/varFreqs/colorsDb/colorsDbSnv.vcf.gz.tbi
+
+# The varFreqs.ra trackDb file is already in human/ (shared for both
+# hg38 and hs1 via the human/trackDb.ra include), so no move was needed.
+# Only colorsDbSnv is expected to render on hs1 - the other varFreqs
+# subtracks have hg38-only data and will silently show nothing there.