89491842e0ec6b2250aa6f6dc2c83c294930e6d6 max Sun May 17 14:38:40 2026 -0700 Add ChinaMAP phase 1 variant frequencies subtrack on hg38 ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short indels). The released VCF is already on GRCh38 with chr-prefixed chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it is served directly via vcfTabix. The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb directory is _chinamap (hidden from hgdownload) and the trackDb stanza has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so the next varFreqsAll combined rebuild picks it up; filter UI is deliberately not added yet (WBBC/TPMI precedent). , refs #36642 diff --git src/hg/makeDb/scripts/varFreqs/databases.tsv src/hg/makeDb/scripts/varFreqs/databases.tsv index 228281014c1..08b7a8e3a37 100644 --- src/hg/makeDb/scripts/varFreqs/databases.tsv +++ src/hg/makeDb/scripts/varFreqs/databases.tsv @@ -1,30 +1,34 @@ # 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 +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/ga100k.indels.vcf.gz AC AF -NPM NPM Singapore /gbdb/hg38/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz AC AF -KOVA KOVA Korea /gbdb/hg38/varFreqs/kova/kova.v7.vcf.gz AC AF +NPM NPM Singapore /gbdb/hg38/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz 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 +# IndiGen dropped: the IGIB IndiGenomes release ships only a VRT variation-type +# bit per record (no AC, AF, or AN in INFO), so it cannot contribute counts to +# the combined track. Re-add only if a future release exposes allele counts. +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 +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 +MGRB MGRB Australia /gbdb/hg38/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz AC . HRC HRC /gbdb/hg38/varFreqs/hrc/hrc.vcf.gz AC AF -MexBB Mexico Biobank /gbdb/hg38/varFreqs/mxb/mxb.freq.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 +Tishkoff180 Tishkoff 180 African WGS /gbdb/hg38/varFreqs/_tishkoff/tishkoff180.vcf.gz AC AF WBBC WBBC China /gbdb/hg38/varFreqs/wbbc/wbbc.vcf.gz AC AF +TPMI TPMI Taiwan /gbdb/hg38/varFreqs/_tpmi/tpmi.vcf.gz AC AF +ChinaMAP China ChinaMAP /gbdb/hg38/varFreqs/_chinamap/chinamap.vcf.gz AC AF