459736686ba7726d2e9bfe63757183b4e8153e53 lrnassar Wed May 13 13:09:18 2026 -0700 varFreqs: set default visibility to hide on all 26 non-summary subtracks. Leaves varFreqsAll on pack (the summary combined-track stays the default view) and the supertrack on hide. Users opt into individual cohorts via the combined-track filter; enabling the supertrack no longer tries to render 25+ vcfTabix tracks at once. Confirmed by Max. refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 7b805e500b9..c8c396e9d12 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -270,295 +270,295 @@ 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/$D/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 - visibility dense + visibility hide priority 0.5 #track me #shortLabel Regeneron Million Exomes 983k WES #longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on #bigDataUrl /gbdb/$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/$D/varFreqs/topmed/topmed10.vcf.gz dataVersion Freeze 10 - visibility dense + visibility hide priority 2 track sfariSparkExomes shortLabel SFARI SPARK 140k WES longLabel Variant Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 - visibility dense + visibility hide 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/$D/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 - visibility dense + visibility hide priority 2.5 html sfariSparkExomes #track mcps #shortLabel Mexico City Prospective Study 10k WGS+141k WES #longLabel Variant Frequencies: Mexico City Prospective Study (MCPS) #tableBrowser off #parent varFreqs on #bigDataUrl /gbdb/$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/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz - visibility dense + visibility hide dataVersion 2025-06-16 priority 5 track alfaVcf shortLabel NCBI ALFA 408k mixed longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz - visibility dense + 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 dense + visibility hide 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/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track swefreq parent varFreqs on - visibility dense + visibility hide type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel Variant Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$D/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track mgrb shortLabel Australia MGRB 4k WGS longLabel Variant Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 - visibility dense + visibility hide # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia 1.7k SNVs longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz - visibility dense + visibility hide dataVersion Pilot 2019 (lifted to hg38, May 2026) track gaspIndel shortLabel GenomeAsia 1.7k Indels longLabel Variant Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.indels.vcf.gz - visibility dense + visibility hide dataVersion Pilot 2019 (lifted to hg38, May 2026) html gasp track abraom shortLabel Brazil ABraOM 1k WGS longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz - visibility dense + visibility hide 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/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz - visibility dense + visibility hide dataVersion IndiGen pilot (Jain 2021) track kova shortLabel Korea KOVA 5.3k mixed longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/kova/kova.v7.vcf.gz - visibility dense + visibility hide 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/$D/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz - visibility dense + visibility hide tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS longLabel Variant Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz - visibility dense + visibility hide dataVersion r1.1 track saudi shortLabel Saudi Genome 302 WGS longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz - visibility dense + visibility hide dataVersion SHGP (figshare 51297884, 2025) track schema shortLabel SCHEMA 121k WES Sz longLabel Variant Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz - visibility dense + 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 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mxb/mxb.freq.vcf.gz - visibility dense + visibility hide dataVersion Nov 2025 (hg38 lift) priority 6 track sgdpFreq shortLabel SGDP 279 WGS longLabel Variant Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz - visibility dense + 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 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz - visibility dense + visibility hide dataVersion R04 (Oct 2025) priority 8 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS longLabel Variant Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz - visibility dense + 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 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz - visibility dense + visibility hide dataVersion Cohen 2022 release priority 9 track colorsDbSnv shortLabel CoLoRSdb 1k LR SNV/Ind longLabel Variant Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz - visibility dense + 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 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz - visibility dense + visibility hide dataVersion Chirmade 2025 release priority 10 track tishkoff180 shortLabel 12 Afr Pops 180 WGS longLabel Variant Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tishkoff/tishkoff180.vcf.gz - visibility dense + visibility hide dataVersion Cell 2023 (hg19 lift) tableBrowser off priority 7.5