366afa4a74c46ec6fb2b667a2902a873feec40cf
max
  Mon Apr 20 23:00:05 2026 -0700
varFreqsAll: rebuild combined bigBed to include GA4K and CoLoRSdb

Regenerate the All Databases Combined track with the two long-read
PacBio subtracks (GA4K 552 samples and CoLoRSdb v1.2.0 1,027 samples)
that were added to varFreqs since the March build. Source count rises
from 21 to 23 databases; final bigBed is 37.7 GB with 1.17B records
and 113 fields. Updates varFreqs.ra filterValues.sources and per-
database AF/AC filters for the two new sources, and databases.tsv
+ varFreqs.txt (build notes).

refs #36642

diff --git src/hg/makeDb/scripts/varFreqs/databases.tsv src/hg/makeDb/scripts/varFreqs/databases.tsv
index b4885fda40f..1f34c503198 100644
--- src/hg/makeDb/scripts/varFreqs/databases.tsv
+++ src/hg/makeDb/scripts/varFreqs/databases.tsv
@@ -1,24 +1,26 @@
 # Database configuration for varFreqsAll combined track
 # key	name	vcf	ac_field	af_field
 # Use "." for fields that don't exist in the VCF
 AllOfUs	AllOfUs	/gbdb/hg38/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz	.	.
 SPARK	SPARK WES	/gbdb/hg38/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz	AC	AF
 SFARI_WGS	SFARI WGS	/gbdb/hg38/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz	AC	AF
 GenomeAsia	GenomeAsia SNVs	/gbdb/hg38/varFreqs/ga100k/ga100k.subst.vcf.gz	AC	AF
 GenomeAsiaIndel	GenomeAsia Indels	/gbdb/hg38/varFreqs/ga100k/All.indels.annot.cont_withmaf.vcf.gz	AC	AF
 KOVA	KOVA Korea	/gbdb/hg38/varFreqs/kova/kova.v7.vcf.gz	AC	AF
 ToMMo	ToMMo Japan	/gbdb/hg38/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz	AC	AF
 IndiGen	IndiGenomes India	/gbdb/hg38/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz	AC	AF
 FinnGen	FinnGen Finland	/gbdb/hg38/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz	AC	AF
 Saudi	Saudi	/gbdb/hg38/varFreqs/saudi/saudi.vcf.gz	AC	AF
 SweGen	SweGen Sweden	/gbdb/hg38/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz	AC	AF
 TOPMed	TOPMed	/gbdb/hg38/varFreqs/topmed/topmed10.vcf.gz	AC	AF
 ABraOM	ABraOM Brazil	/gbdb/hg38/varFreqs/abraom/abraom.vcf.gz	.	AF
 ALFA	ALFA	/gbdb/hg38/varFreqs/alfa/ALFA.vcf.gz	.	AF_GLB
 MGRB	MGRB Australia	/gbdb/hg38/varFreqs/mgrb/MGRB.phase3.GRCh38.norm.vcf.gz	AC	AF
 HRC	HRC	/gbdb/hg38/varFreqs/hrc/hrc.vcf.gz	AC	AF
 MexBB	Mexico Biobank	/gbdb/hg38/varFreqs/mxb/mxb.freq.vcf.gz	AC	AF
 SGDP	SGDP	/gbdb/hg38/varFreqs/sgdpFreq/sgdp.freq.vcf.gz	AC	AF
 HGDP1kG	gnomAD HGDP+1kG	/gbdb/hg38/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz	AC	AF
 GREGoR	GREGoR	/gbdb/hg38/varFreqs/gregor/gregor.vcf.gz	AC	AF
 SCHEMA	SCHEMA	/gbdb/hg38/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz	AC	AF
+GA4K	GA4K PacBio LR	/gbdb/hg38/varFreqs/ga4k/ga4kSnv.vcf.gz	AC	AF
+CoLoRSdb	CoLoRSdb PacBio LR	/gbdb/hg38/varFreqs/colorsDb/colorsDbSnv.vcf.gz	AC	AF