5c88f2b10f443d95e3f9c8e4bbc81534b78d9222
max
  Thu May 21 00:40:38 2026 -0700
varFreqs: rename supertrack to "SNV Frequencies"; add GoNL (Netherlands, ~13x SR) to databases.tsv and to the varFreqsAll filter UI so the next combined-track rebuild picks it up. refs #36642

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

diff --git src/hg/makeDb/doc/hg38/varFreqs.txt src/hg/makeDb/doc/hg38/varFreqs.txt
index 1563d8d603f..5ccb20fda1b 100644
--- src/hg/makeDb/doc/hg38/varFreqs.txt
+++ src/hg/makeDb/doc/hg38/varFreqs.txt
@@ -862,15 +862,18 @@
 ( bcftools view -h multisample.parents_only.info_only.vcf.gz; \
   bcftools view -H multisample.parents_only.info_only.vcf.gz \
     | awk -F'\t' 'BEGIN{while((getline k < "keep.chroms.txt") > 0) ok[k]=1} ok[$1]' \
 ) | bgzip -@ 8 -c > gonl.preNorm.vcf.gz
 tabix -p vcf gonl.preNorm.vcf.gz
 # 31,114,481 input records -> 30,904,161 kept (0.68% dropped, all on
 # decoy / EBV contigs not present in hg38). Max AN = 996, matching 498
 # diploid parents.
 # Split multiallelic sites and left-align indels against the hg38 reference.
 ln -sf /hive/data/genomes/hg38/bed/varFreqs/all/hg38.fa hg38.fa
 ln -sf /hive/data/genomes/hg38/bed/varFreqs/all/hg38.fa.fai hg38.fa.fai
 bcftools norm -f hg38.fa -m-any --threads 8 gonl.preNorm.vcf.gz -Oz -o gonl.vcf.gz
 tabix -p vcf gonl.vcf.gz
 # norm stats: 30,904,161 -> 36,363,474 records (2,629,361 multiallelic
 # sites split, 3,559,402 indels left-realigned, 0 dup/mismatch).
+# GoNL added to databases.tsv as well, so the next mergeAndAnnotate.sh
+# run will pick it up into varFreqsAll.bb. The current /gbdb _all
+# bigBed predates GoNL.