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 @@ -67,137 +67,39 @@ 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/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track swefreq @@ -259,15 +161,135 @@ longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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