442e433a90b25deb87f10e6cf1b7b608bb0a6d67 max Sat Sep 26 21:56:06 2026 -0700 sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424 diff --git src/hg/makeDb/scripts/varFreqs/databases.tsv src/hg/makeDb/scripts/varFreqs/databases.tsv index fd9cafb6da8..6d38fb99e11 100644 --- src/hg/makeDb/scripts/varFreqs/databases.tsv +++ src/hg/makeDb/scripts/varFreqs/databases.tsv @@ -1,51 +1,54 @@ # Database configuration for varFreqsAll combined track # key name vcf ac_field af_field is_disease disease_role default_an skip_top_ranking # Use "." for fields that don't exist in the VCF # is_disease=1: cohort assembled to study a disease (autism, schizophrenia, rare disease). # disease_role: for a disease cohort with NO affected/unaffected population split, what is # the whole cohort? "affected" (e.g. GA4K rare-disease probands) feeds the affected # summary; blank means use the per-population phenotype tags in populations.tsv instead. # default_an: fallback cohort allele number used when AC is empty but AF is present (or # vice versa). Lets AF-only cohorts contribute to the pooled affectedAF/backgroundAF # denominator. Leave blank if the cohort always ships both AC and AF. # skip_top_ranking=1: cohort's per-source AF is unreliable for the Top-3 mouseOver # ranking and should not be ranked. Currently set for SGDP and SVatalog, whose # VCFs encode AC/AN per genotyped individual (small N, AF defaults near 0.5), so # they would always rank #1 with a meaningless inflated value. They still # contribute to pooled AC/AN/AF and appear in the Sources list. # TOPMed is is_disease=0: it is an NHLBI population/biobank reference (used like gnomAD), # not an affected-disease case cohort, and ships no affected/unaffected label. AllOfUs AllOfUs /gbdb/hg38/varFreqs/_allofus/allOfUs.locAncFreq.vcf.gz . . 0 SPARK SFARI SPARK WES /gbdb/hg38/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz AC AF 1 -SFARI_WGS SFARI SPARK WGS /gbdb/hg38/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz AC AF 1 +SFARI_WGS SFARI SPARK iWGS v1.1 Pilot /gbdb/hg38/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz AC AF 1 +# SPARK45k: SFARI SPARK WGS 2026_08, 45,178 genomes. The merge reads a copy without the +# 25M FILTER=NonHumanIns insertions (oral bacteria DNA from the saliva samples, see makeDoc). +SPARK45k SFARI SPARK 45k WGS /hive/data/genomes/hg38/bed/varFreqs/sparkWgs45k/pvcfSites/sparkWgs45kAsd.noNonHumanIns.vcf.gz AC AF 1 GenomeAsia GenomeAsia SNVs /gbdb/hg38/varFreqs/ga100k/ga100k.subst.vcf.gz AC AF 0 GenomeAsiaIndel GenomeAsia Indels /gbdb/hg38/varFreqs/ga100k/ga100k.indels.vcf.gz AC AF 0 NPM NPM Singapore /gbdb/hg38/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz AC AF 0 KOVA KOVA Korea /gbdb/hg38/varFreqs/_kova/kova.v7.vcf.gz AC AF 0 ToMMo ToMMo Japan /gbdb/hg38/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz AC AF 0 # 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 0 Saudi Saudi /gbdb/hg38/varFreqs/saudi/saudi.vcf.gz AC AF 0 SweGen SweGen Sweden /gbdb/hg38/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz AC AF 0 TOPMed TOPMed /gbdb/hg38/varFreqs/_topmed/topmed10.vcf.gz AC AF 0 ABraOM ABraOM Brazil /gbdb/hg38/varFreqs/abraom/abraom.vcf.gz . AF 0 2342 0 ALFA ALFA /gbdb/hg38/varFreqs/alfa/ALFA.vcf.gz . AF_GLB 0 816000 0 MGRB MGRB Australia /gbdb/hg38/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz AC . 0 HRC HRC /gbdb/hg38/varFreqs/hrc/hrc.vcf.gz AC AF 0 # MexBB and TPMI moved to the array-based track (databases_array.tsv): both are # genotyping-array cohorts and are kept out of the WGS/WES varFreqsAll track. SGDP SGDP /gbdb/hg38/varFreqs/sgdpFreq/sgdp.freq.vcf.gz AC AF 0 1 HGDP1kG gnomAD HGDP+1kG /gbdb/hg38/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz AC AF 0 GREGoR GREGoR /gbdb/hg38/varFreqs/gregor/gregor.vcf.gz AC AF 1 SCHEMA SCHEMA /gbdb/hg38/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz AC AF 1 GA4K GA4K PacBio LR /gbdb/hg38/varFreqs/ga4k/ga4kSnv.vcf.gz AC AF 1 affected CoLoRSdb CoLoRSdb PacBio LR /gbdb/hg38/varFreqs/colorsDb/colorsDbSnv.vcf.gz AC AF 0 SVatalog SVatalog 101 10XG SR /gbdb/hg38/varFreqs/svatalog/svatalog.vcf.gz AC AF 0 1 Tishkoff180 Tishkoff 180 African WGS /gbdb/hg38/varFreqs/_tishkoff/tishkoff180.vcf.gz AC AF 0 WBBC WBBC China /gbdb/hg38/varFreqs/wbbc/wbbc.vcf.gz AC AF 0 ChinaMAP China ChinaMAP /gbdb/hg38/varFreqs/_chinamap/chinamap.vcf.gz AC AF 0 GenomeIndia GenomeIndia 9.7k WGS /gbdb/hg38/varFreqs/_genomeindia/genomeindia.vcf.gz AC AF 0 GoNL GoNL Netherlands ~13x SR /gbdb/hg38/varFreqs/gonl/gonl.vcf.gz AC AF 0 HostSeq HostSeq Canada /gbdb/hg38/varFreqs/hostseq/hostseq.vcf.gz AC AF 0