99ae46aca64e768875e6cbb2a232a0648bea5344 max Fri May 15 10:13:21 2026 -0700 varFreqs: prefix non-downloadable /gbdb subdirs with "_" so hgdownload rsync skips them; update bigDataUrl paths and Data Access wording on description pages for topmed, allofus, sfariSparkExomes/sfariSparkWgs, and mxbFreq. Combined varFreqsAll.bb moved into _all/. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 923573b25d4..2bb10d09a3a 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,29 +1,29 @@ track varFreqs shortLabel Variant Frequencies longLabel Variant Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on track varFreqsAll shortLabel All Databases Combined longLabel Variant Frequencies: All Databases Combined with Consequence Annotations type bigBed 9 + parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/varFreqsAll.bb + bigDataUrl /gbdb/$D/varFreqs/_all/varFreqsAll.bb visibility pack itemRgb on maxWindowToDraw 5000000 priority 0.1 mouseOver <b>Var:</b> $name<br><b>AA change:</b> $aaChange<br><b>Var type:</b> $varType<br><b>Conseq:</b> $consequence<br><b>Max AF:</b> $maxAF<br><b>Total AC:</b> $totalAC<br><b>Sources:</b> $sources # Variant type and consequence filters filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence # Source database filter filterValues.sources AllOfUs|AllOfUs,SPARK|SPARK WES,SFARI_WGS|SFARI WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,KOVA|KOVA Korea,ToMMo|ToMMo Japan,IndiGen|IndiGenomes India,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,MexBB|Mexico Biobank,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,NPM|NPM Singapore filterType.sources multipleListOr filterLabel.sources Source Database @@ -268,76 +268,76 @@ filterByRange.NPMAF_Indian on filterLabel.NPMAF_Indian NPM Singapore Indian AF filterByRange.NPMAC_Chinese on filterLabel.NPMAC_Chinese NPM Singapore Chinese AC filterByRange.NPMAC_Malay on filterLabel.NPMAC_Malay NPM Singapore Malay AC filterByRange.NPMAC_Indian on filterLabel.NPMAC_Indian NPM Singapore Indian AC skipEmptyFields on track allofus shortLabel AllOfUs v7 245k WGS longLabel Variant Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility dense tableBrowser off priority 0.5 #track me #shortLabel Regeneron Million Exomes 983k WES #longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/me/me.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/$D/varFreqs/topmed/topmed10.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_topmed/topmed10.vcf.gz dataVersion Freeze 10 visibility dense tableBrowser off priority 2 track sfariSparkExomes shortLabel SFARI SPARK 140k WES longLabel Variant Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 visibility dense tableBrowser off 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/$D/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 visibility dense priority 2.5 html sfariSparkExomes tableBrowser off #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/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) @@ -356,85 +356,86 @@ track wbbc shortLabel China WBBC 4.5k WGS longLabel Variant Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz visibility dense dataVersion Phase I v20210103 priority 5.5 track tpmi shortLabel Taiwan TPMI Axiom array longLabel Variant Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/tpmi/tpmi.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz visibility dense dataVersion Axiom TPM1 2022-06 priority 5.6 + tableBrowser off track alfaVcf shortLabel NCBI ALFA 408k mixed 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 dense 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 dense type vcfTabix shortLabel FinnGen R12 500k imputed longLabel Variant Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 - bigDataUrl /gbdb/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track ukbb parent varFreqs on visibility dense type vcfTabix shortLabel UK Biobank 361k imputed longLabel Variant Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed priority 4.6 bigDataUrl /gbdb/$D/varFreqs/ukbb/ukbb.vcf.gz dataVersion Neale Lab R2 08-2018 track swefreq parent varFreqs on visibility dense type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel Variant Frequencies: Sweden SweGen - 1k WGS priority 4.7 - bigDataUrl /gbdb/$D/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track mgrb shortLabel Australia MGRB 4k WGS longLabel Variant Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/mgrb/MGRB.phase3.GRCh38.norm.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 visibility dense # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia 1.7k SNVs longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility dense dataVersion Pilot 2019 (lifted to hg38, May 2026) track gaspIndel @@ -458,41 +459,41 @@ track indigenomes shortLabel India IndiGenomes 1k WGS longLabel Variant Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility dense dataVersion IndiGen pilot (Jain 2021) track kova shortLabel Korea KOVA 5.3k mixed longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/kova/kova.v7.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz visibility dense tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz + bigDataUrl /gbdb/$D/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility dense tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS longLabel Variant Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz visibility dense dataVersion r1.1 track saudi shortLabel Saudi Genome 302 WGS @@ -508,31 +509,31 @@ longLabel Variant Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility dense dataVersion 2022 priority 4.9 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track mxbFreq shortLabel Mexico Biobank 6k Array longLabel Variant Frequencies: Mexico Biobank - 6,011 individuals, genotyping array type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/mxb/mxb.freq.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_mxb/mxb.freq.vcf.gz visibility dense dataVersion Nov 2025 (hg38 lift) tableBrowser off priority 6 track sgdpFreq shortLabel SGDP 279 WGS longLabel Variant Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility dense dataVersion 2016-12-07 (hg38 lift) priority 7 @@ -579,21 +580,21 @@ track svatalogSnv shortLabel SVatalog 101 WGS longLabel Variant Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz visibility dense dataVersion Chirmade 2025 release priority 10 track tishkoff180 shortLabel 12 Afr Pops 180 WGS longLabel Variant Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/tishkoff/tishkoff180.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/_tishkoff/tishkoff180.vcf.gz visibility dense dataVersion Cell 2023 (hg19 lift) tableBrowser off priority 7.5