ec5c73f4dc3ef4beae16fa1c12b7e5bf872bb73d lrnassar Tue May 5 15:04:39 2026 -0700 varFreqs: fix gaspIndel bigDataUrl after Max's GenomeAsia hg38 lift; add Tishkoff180 to combined-track filter UI; sync databases.tsv with deployed bigBed; minor description-page corrections. refs #36642 GenomeAsia hg38 lift (May 5 2026, by Max): - gaspIndel.bigDataUrl was pointing at the old GRCh37 filename "All.indels.annot.cont_withmaf.vcf.gz" which was renamed to "ga100k.indels.vcf.gz" during the lift; this left the gaspIndel track broken on the sandbox until the trackdb stanza was updated to match. - gasp/gaspIndel dataVersion strings updated from "Pilot 2019 (GRCh37 - to be lifted)" to "Pilot 2019 (lifted to hg38, May 2026)". - databases.tsv: also updated GenomeAsiaIndel path to ga100k.indels.vcf.gz so the next varFreqsAll rebuild reads from the lifted file. Tishkoff180 in varFreqsAll.bb but unfilterable (fresh-eyes audit finding): - Added Tishkoff180 to filterValues.sources and added filterByRange.Tishkoff180AF / Tishkoff180AC entries. - Added Tishkoff180 (and SVatalog) rows to databases.tsv to match the deployed bigBed (which already has those columns). Description-page corrections: - varFreqsAll.html: "20 population databases" -> "25 source databases" (matches actual count); HGDP+1kG bullet "European" -> "Non-Finnish European" to disambiguate from Finnish (gnomAD's nfe). - varFreqs.html: GenomeAsia row in the Available Datasets table updated from 3 to 7 sub-populations (NEA/SEA/SAS plus the previously hidden OCE/AMR/AFR/WER) so the table matches what the data exposes once Max's rebuild populates the new filter columns. - KOVA longLabel: "1.9k WGS+3.5k WES" -> "1.9k WGS+3.4k WES" (3.4k is correct per Lee 2017 and kova.html). 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