7fd4df639618f431e81244f1c0ad911e4dcb0bd5 max Wed Jan 28 04:56:31 2026 -0800 adding Australia Biobank and fixing up NCBI Alfa docs, refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 23a7dc047cc..937ecb08520 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,295 +1,306 @@ track varFreqs shortLabel Variant Frequencies longLabel Variant Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on track allofus shortLabel AllOfUs v7 245k WGS longLabel Variant Frequencies: AllOfUs - v7 245k WGS, only with allele count >= 20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility pack priority 0.5 track me shortLabel Regeneron Million Exomes 983k WES longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz visibility pack type vcfTabix hapClusterEnabled true dataVersion 10/04/2023, v1.1.3 tableBrowser off priority 1 track topmed shortLabel NHLBI TOPMED 10 151k WGS longLabel Variant Frequencies: NHLBI TOPMED - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/topmed/topmed10.vcf.gz dataVersion Freeze 10 visibility pack priority 2 track sfariSparkExomes shortLabel SFARI Spark 140k WES longLabel Variant Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 visibility pack priority 2.5 track sfariSparkWgs shortLabel SFARI Spark 12k WGS longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 visibility pack priority 2.5 track mcps shortLabel Mexico City Prospective Study 10k WGS+141k WES longLabel Variant Frequencies: Mexico City Prospective Study (MCPS) tableBrowser off parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz visibility pack type vcfTabix dataVersion May 2023 (v1.2.0) priority 3 track tommo60kjpn shortLabel Japan ToMMO 61k WGS longLabel Variant Frequencies: Japan 61k - ToMMO SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility pack dataVersion 2025-06-16 priority 5 track alfaVcf shortLabel NCBI ALFA 408k WGS/WES/array longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz visibility pack dataVersion R4 priority 4.1 url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track finngen parent varFreqs on visibility pack type vcfTabix shortLabel Finnland Finngen 500k imputed longLabel Variant Frequencies: Finnland Finngen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track swefreq parent varFreqs on visibility pack type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel Variant Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$D/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off + track mgrb + shortLabel Australie MGRB 4k WGS + longLabel Variant Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/mgrb/MGRB.phase3.GRCh38.norm.vcf.gz + dataVersion Phase 3 + visibility pack + # no downloads as per Matt Hobbs email Jan 28 2026 + tableBrowser off + track gasp shortLabel GenomeAsia Pilot Subs 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility pack track gaspIndel shortLabel GenomeAsia Pilot Indels 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/All.indels.annot.cont_withmaf.vcf.gz visibility pack track abraom shortLabel Brazil ABraOM 1k WGS longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility pack dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS longLabel Variant Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility pack track kova shortLabel Korea KOVA 1.9k WGS+3.5k WES longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.5k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/kova/kova.v7.vcf.gz visibility pack tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility pack tableBrowser off dataVersion r5.3.2 track saudi shortLabel Saudi Genome Project 302 WGS longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility pack track schema shortLabel SCHEMA Schizophrenia 121k WES longLabel Variant Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility pack dataVersion 2022 priority 4.9 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track varFreqsAll shortLabel All Databases Combined longLabel Variant Frequencies: All Databases Combined with Consequence Annotations type bigBed 9 + parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/varFreqsAll.bb visibility dense itemRgb on maxWindowToDraw 5000000 # Variant type and consequence filters filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,.|Intergenic filterLabel.consequence Consequence filterValues.sources aou|AllOfUs,spk|SPARK_iWES,wgs|SFARI_WGS,ga|GenomeAsia100K,kov|KOVA,tom|ToMMo,mcp|MCPS,ind|IndiGenomes,fin|FinnGen,sau|Saudi,swe|SweGen,top|TOPMed,abr|ABraOM filterType.sources multipleListOr filterLabel.sources Source Database # Length filters filterByRange.refLen on filterLabel.refLen Reference Length filterByRange.altLen on filterLabel.altLen Alternate Length filterByRange.varLen on filterLabel.varLen Length Change # Max AF filter filterByRange.maxAF on filterLabel.maxAF Max Allele Frequency filterLimits.maxAF 0:1 # Per-database AF filters filterByRange.aouAF on filterLabel.aouAF AllOfUs AF filterByRange.spkAF on filterLabel.spkAF SPARK AF filterByRange.wgsAF on filterLabel.wgsAF SFARI WGS AF filterByRange.gaAF on filterLabel.gaAF GenomeAsia AF filterByRange.kovAF on filterLabel.kovAF KOVA AF filterByRange.tomAF on filterLabel.tomAF ToMMo AF filterByRange.mcpAF on filterLabel.mcpAF MCPS AF filterByRange.indAF on filterLabel.indAF IndiGenomes AF filterByRange.finAF on filterLabel.finAF FinnGen AF filterByRange.sauAF on filterLabel.sauAF Saudi AF filterByRange.sweAF on filterLabel.sweAF SweGen AF filterByRange.topAF on filterLabel.topAF TOPMed AF filterByRange.abrAF on filterLabel.abrAF ABraOM AF # Per-database AC filters filterByRange.aouAC on filterLabel.aouAC AllOfUs AC filterByRange.spkAC on filterLabel.spkAC SPARK AC filterByRange.wgsAC on filterLabel.wgsAC SFARI WGS AC filterByRange.gaAC on filterLabel.gaAC GenomeAsia AC filterByRange.kovAC on filterLabel.kovAC KOVA AC filterByRange.tomAC on filterLabel.tomAC ToMMo AC filterByRange.mcpAC on filterLabel.mcpAC MCPS AC filterByRange.indAC on filterLabel.indAC IndiGenomes AC filterByRange.finAC on filterLabel.finAC FinnGen AC filterByRange.sauAC on filterLabel.sauAC Saudi AC filterByRange.sweAC on filterLabel.sweAC SweGen AC filterByRange.topAC on filterLabel.topAC TOPMed AC filterByRange.abrAC on filterLabel.abrAC ABraOM AC # Population-specific AF filters (AllOfUs) filterByRange.aouAF_AFR on filterLabel.aouAF_AFR AllOfUs AFR AF filterByRange.aouAF_AMR on filterLabel.aouAF_AMR AllOfUs AMR AF filterByRange.aouAF_EAS on filterLabel.aouAF_EAS AllOfUs EAS AF filterByRange.aouAF_EUR on filterLabel.aouAF_EUR AllOfUs EUR AF filterByRange.aouAF_SAS on filterLabel.aouAF_SAS AllOfUs SAS AF # Population-specific AF filters (GenomeAsia) filterByRange.gaAF_NEA on filterLabel.gaAF_NEA GenomeAsia NEA AF filterByRange.gaAF_SEA on filterLabel.gaAF_SEA GenomeAsia SEA AF filterByRange.gaAF_SAS on filterLabel.gaAF_SAS GenomeAsia SAS AF # Population-specific AF filters (MCPS) filterByRange.mcpAF_AFR on filterLabel.mcpAF_AFR MCPS AFR AF filterByRange.mcpAF_EUR on filterLabel.mcpAF_EUR MCPS EUR AF filterByRange.mcpAF_IMX on filterLabel.mcpAF_IMX MCPS Indigenous MX AF