5059707121527ccfa37fba0e1bc2617ab15d34b2 max Tue Jan 27 08:39:05 2026 -0800 converting NCBI ALFA to VCF format, necessary for varFreqs merge, refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 39aca767481..23a7dc047cc 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,273 +1,295 @@ 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/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility pack dataVersion 2025-06-16 priority 5 - track ALFA - compositeTrack on + track alfaVcf + shortLabel NCBI ALFA 408k WGS/WES/array + longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants + type vcfTabix parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz visibility pack - itemRgb on - type bigBed 9 + . - shortLabel NCBI ALFA 408k WGS/WES/array - longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array - mouseOverField frequency - html ALFA.html - filter.score 10 - priority 4 dataVersion R4 - - track ALFA_GLB - parent ALFA on - shortLabel NCBI ALFA: Global - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_GLB.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_EUR - parent ALFA on - shortLabel NCBI ALFA: European - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_EUR.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_AFA - parent ALFA on - shortLabel NCBI ALFA: African American - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFA.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_AFO - parent ALFA on - shortLabel NCBI ALFA: African Others - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFO.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_AFR - parent ALFA on - shortLabel NCBI ALFA: African - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFR.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_EAS - parent ALFA on - shortLabel NCBI ALFA: East Asian - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_EAS.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_SAS - parent ALFA on - shortLabel NCBI ALFA: South Asian - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_SAS.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_OAS - parent ALFA on - shortLabel NCBI ALFA: Other Asian - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_OAS.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_ASN - parent ALFA on - shortLabel NCBI ALFA: Asian - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_ASN.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_LAC - parent ALFA on - shortLabel NCBI ALFA: Latin American 1 - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_LAC.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_LEN - parent ALFA on - shortLabel NCBI ALFA: Latin American 2 - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_LEN.bb - type bigBed 9 + . - url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab - urlLabel NCBI Variation Page - - track ALFA_OTR - parent ALFA on - shortLabel NCBI ALFA: Other - bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_OTR.bb - type bigBed 9 + . + priority 4.1 url https://www.ncbi.nlm.nih.gov/snp/$$#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 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