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