68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa lrnassar Mon Jun 1 14:40:45 2026 -0700 varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 03108bfab9b..a2c2053d2e8 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,26 +1,26 @@ track varFreqs shortLabel SNV Frequencies longLabel SNV 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 + longLabel SNV Frequencies: All Databases Combined with Consequence Annotations type bigBed 9 + parent varFreqs on 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> $sources # Source database filter filterValues.sources AllOfUs|AllOfUs,SPARK|SPARK WES,SFARI_WGS|SFARI WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR filterType.sources multipleListOr filterLabel.sources Source Database # Variant type and consequence filters filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type @@ -317,31 +317,31 @@ filterByRange.SFARI_WGSAC_NON_AUT on filterLabel.SFARI_WGSAC_NON_AUT SFARI WGS Non-ASD family AC # SCHEMA schizophrenia case/control (summed across analysis groups) filterByRange.SCHEMAAF_CASE on filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF filterByRange.SCHEMAAF_CTRL on filterLabel.SCHEMAAF_CTRL SCHEMA Control AF filterByRange.SCHEMAAC_CASE on filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC filterByRange.SCHEMAAC_CTRL on filterLabel.SCHEMAAC_CTRL SCHEMA Control AC skipEmptyFields on track varFreqsDisease shortLabel Disease-related Databases Combined - longLabel Variant Frequencies: Disease-related cohorts combined (autism, schizophrenia, rare disease, NHLBI heart/lung/blood) + longLabel SNV Frequencies: Disease-related cohorts combined (autism, schizophrenia, rare disease, NHLBI heart/lung/blood) type bigBed 9 + parent varFreqs off bigDataUrl /gbdb/$D/varFreqs/_disease/varFreqsDisease.bb visibility hide itemRgb on maxWindowToDraw 5000000 priority 0.15 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> $sources filterValues.sources SPARK|SPARK WES,SFARI_WGS|SFARI WGS,TOPMed|TOPMed,SCHEMA|SCHEMA,GREGoR|GREGoR,GA4K|GA4K PacBio LR filterType.sources multipleListOr filterLabel.sources Source Database filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr @@ -415,31 +415,31 @@ filterLabel.GREGoRAF_AFF GREGoR Affected AF filterByRange.GREGoRAF_UNA on filterLabel.GREGoRAF_UNA GREGoR Unaffected AF filterByRange.GREGoRAF_UNK on filterLabel.GREGoRAF_UNK GREGoR Unknown AF filterByRange.GREGoRAC_AFF on filterLabel.GREGoRAC_AFF GREGoR Affected AC filterByRange.GREGoRAC_UNA on filterLabel.GREGoRAC_UNA GREGoR Unaffected AC filterByRange.GREGoRAC_UNK on filterLabel.GREGoRAC_UNK GREGoR Unknown AC skipEmptyFields on track varFreqsArray shortLabel Genotyping Array Databases Combined - longLabel Variant Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed) + longLabel SNV Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed) type bigBed 9 + parent varFreqs off bigDataUrl /gbdb/$D/varFreqs/_array/varFreqsArray.bb visibility hide itemRgb on maxWindowToDraw 5000000 priority 0.2 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> $sources filterValues.sources TPMI|TPMI Taiwan,MexBB|Mexico Biobank,UKBB|UK Biobank imputed filterType.sources multipleListOr filterLabel.sources Source Database filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr @@ -459,367 +459,367 @@ filterLabel.TPMIAF TPMI Taiwan AF filterByRange.MexBBAF on filterLabel.MexBBAF Mexico Biobank AF filterByRange.UKBBAF on filterLabel.UKBBAF UK Biobank imputed AF filterByRange.TPMIAC on filterLabel.TPMIAC TPMI Taiwan AC filterByRange.MexBBAC on filterLabel.MexBBAC Mexico Biobank AC filterByRange.UKBBAC on filterLabel.UKBBAC UK Biobank imputed AC skipEmptyFields on track allofus shortLabel AllOfUs v7 245k WGS - longLabel Variant Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 + longLabel SNV Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility hide tableBrowser off priority 0.5 #track me #shortLabel Regeneron Million Exomes 983k WES - #longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS + #longLabel SNV Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/me/me.freq.vcf.gz #visibility pack #type vcfTabix #hapClusterEnabled true #dataVersion 10/04/2023, v1.1.3 #tableBrowser off #priority 1 track topmed shortLabel NHLBI TOPMed 10 151k WGS - longLabel Variant Frequencies: NHLBI TOPMed - 151k WGS + longLabel SNV Frequencies: NHLBI TOPMed - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_topmed/topmed10.vcf.gz dataVersion Freeze 10 tableBrowser off visibility hide priority 2 track sfariSparkExomes shortLabel SFARI SPARK 140k WES - longLabel Variant Frequencies: SFARI SPARK - 140k WES + longLabel SNV Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 tableBrowser off visibility hide priority 2.5 track sfariSparkWgs shortLabel SFARI SPARK 12k WGS - longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS + longLabel SNV Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 visibility hide 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) + #longLabel SNV Frequencies: Mexico City Prospective Study (MCPS) #tableBrowser off #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) #priority 3 track tommo60kjpn shortLabel Japan ToMMo 61k WGS - longLabel Variant Frequencies: Japan 61k - ToMMo SNV+Indels + longLabel SNV Frequencies: Japan 61k - ToMMo SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility hide dataVersion 2025-06-16 priority 5 track wbbc shortLabel China WBBC 4.5k WGS - longLabel Variant Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups + longLabel SNV Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz visibility hide dataVersion Phase I v20210103 priority 5.5 track chinamap shortLabel China ChinaMAP 10.5k WGS - longLabel Variant Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population + longLabel SNV Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_chinamap/chinamap.vcf.gz visibility hide dataVersion Phase 1 (v2020-03.beta) priority 5.55 tableBrowser off track tpmi shortLabel Taiwan TPMI Axiom array - longLabel Variant Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese + longLabel SNV Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz visibility hide dataVersion Axiom TPM1 2022-06 priority 5.6 tableBrowser off track alfaVcf shortLabel NCBI ALFA 408k mixed - longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants + longLabel SNV Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz visibility hide 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 hide type vcfTabix shortLabel FinnGen R12 500k imputed - longLabel Variant Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS + longLabel SNV Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/_finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track ukbb parent varFreqs on visibility hide type vcfTabix shortLabel UK Biobank 361k imputed - longLabel Variant Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed + longLabel SNV Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed priority 4.6 bigDataUrl /gbdb/$D/varFreqs/ukbb/ukbb.vcf.gz dataVersion Neale Lab R2 08-2018 track swefreq parent varFreqs on visibility hide type vcfTabix shortLabel Sweden SweGen 1k WGS - longLabel Variant Frequencies: Sweden SweGen - 1k WGS + longLabel SNV Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track gonl parent varFreqs on visibility hide type vcfTabix shortLabel Netherlands GoNL 498 WGS - longLabel Variant Frequencies: Genome of the Netherlands - 250 Dutch trios + longLabel SNV Frequencies: Genome of the Netherlands - 250 Dutch trios priority 4.75 bigDataUrl /gbdb/$D/varFreqs/gonl/gonl.vcf.gz dataVersion GRCh38 1.0 track mgrb shortLabel Australia MGRB 4k WGS - longLabel Variant Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS + longLabel SNV Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 visibility hide # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia 1.7k SNVs - longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions + longLabel SNV Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility hide dataVersion Pilot 2019 (lifted to hg38, May 2026) track gaspIndel shortLabel GenomeAsia 1.7k Indels - longLabel Variant Frequencies: GenomeAsia Pilot - Indels + longLabel SNV Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.indels.vcf.gz visibility hide dataVersion Pilot 2019 (lifted to hg38, May 2026) html gasp track abraom shortLabel Brazil ABraOM 1k WGS - longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals + longLabel SNV Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility hide dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS - longLabel Variant Frequencies: IndiGenomes India - 1,029 samples + longLabel SNV Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility hide dataVersion IndiGen pilot (Jain 2021) track genomeindia shortLabel India GenomeIndia 9.7k WGS - longLabel Variant Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) + longLabel SNV Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_genomeindia/genomeindia.vcf.gz visibility hide dataVersion 9768GI_SummaryStats (Apr 2025) priority 4.8 track kova shortLabel Korea KOVA 5.3k mixed - longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES + longLabel SNV Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz visibility hide tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS - longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples + longLabel SNV Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility hide tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS - longLabel Variant Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) + longLabel SNV Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz visibility hide dataVersion r1.1 track saudi shortLabel Saudi Genome 302 WGS - longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples + longLabel SNV Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility hide dataVersion SHGP (figshare 51297884, 2025) track schema shortLabel SCHEMA 121k WES Sz - longLabel Variant Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls + longLabel SNV Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility hide dataVersion 2022 priority 4.9 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track mxbFreq shortLabel Mexico Biobank 6k Array - longLabel Variant Frequencies: Mexico Biobank - 6,011 individuals, genotyping array + longLabel SNV Frequencies: Mexico Biobank - 6,011 individuals, genotyping array type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mxb/mxb.freq.vcf.gz visibility hide 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 + longLabel SNV Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility hide dataVersion 2016-12-07 (hg38 lift) priority 7 track gregor shortLabel GREGoR R4 3.6k WGS - longLabel Variant Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families + longLabel SNV Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz visibility hide dataVersion R04 (Oct 2025) priority 8 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS - longLabel Variant Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations + longLabel SNV Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz visibility hide dataVersion v3.1.2 priority 8 track ga4kSnv shortLabel GA4K 552 PacBio LR - longLabel Variant Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD + longLabel SNV Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz visibility hide dataVersion Cohen 2022 release priority 9 track colorsDbSnv shortLabel CoLoRSdb 1k LR SNV/Ind - longLabel Variant Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset + longLabel SNV Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz visibility hide dataVersion v1.2.0 priority 9.5 track svatalogSnv shortLabel SVatalog 101 WGS - longLabel Variant Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs + longLabel SNV Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz visibility hide 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) + longLabel SNV Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tishkoff/tishkoff180.vcf.gz visibility hide dataVersion Cell 2023 (hg19 lift) tableBrowser off priority 7.5