986c4ede954e44904eb314772fb2cf83a48d307c max Wed May 6 06:24:47 2026 -0700 varFreqs: lift GenomeAsia (gasp + gaspIndel) GRCh37 -> hg38 Both subtracks were served at /gbdb/hg38/ but the upstream callset is GRCh37 (caught in QA, see #36642 note 2026-05-04). Lifted with CrossMap using hg19ToHg38.over.chain.gz; recipe matches tishkoff180 / mxbFreq. gasp (SNVs): 66,236,516 -> 66,222,771 (99.98%; 6,240 unmapped + 7,505 alt/random) gaspIndel: 4,415,156 -> 4,410,871 (99.90%; 3,332 unmapped + 953 alt/random) New driver script: scripts/varFreqs/gaspLift.sh. gaspIndel bigDataUrl renamed from All.indels.annot.cont_withmaf.vcf.gz to ga100k.indels.vcf.gz (old name was a verbatim copy of the upstream download name). varFreqsAll combined bigBed regenerated to fold in the corrected coordinates (36.5 GB, 1,166,451,644 items, 125 fields). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/scripts/varFreqs/databases.tsv src/hg/makeDb/scripts/varFreqs/databases.tsv index 1f34c503198..142589ff57b 100644 --- src/hg/makeDb/scripts/varFreqs/databases.tsv +++ src/hg/makeDb/scripts/varFreqs/databases.tsv @@ -1,26 +1,28 @@ # 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 +GenomeAsiaIndel GenomeAsia Indels /gbdb/hg38/varFreqs/ga100k/ga100k.indels.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 +SVatalog SVatalog 101 10XG SR /gbdb/hg38/varFreqs/svatalog/svatalog.vcf.gz AC AF +Tishkoff180 Tishkoff 180 African WGS /gbdb/hg38/varFreqs/tishkoff/tishkoff180.vcf.gz AC AF