21e8af7d071bb2294f0cf682ac871c63a5a5332d lrnassar Sat Jun 13 05:00:09 2026 -0700 varFreqs: reorder subtrack priorities A-Z by shortLabel. Combined tracks keep their order: Population reference (0.1), Disease cohorts (0.11), Genotyping Array Databases Combined (0.2). The 32 per-project subtracks get integer priorities 1..32 sorted alphabetically by shortLabel (case-insensitive). Adds explicit priority to the 9 subtracks that lacked one (abraom, gasp, gaspIndel, hrc, indigenomes, kova, mgrb, npm, saudi). refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 865e6164400..7d2d7444cf1 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -728,361 +728,370 @@ 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 SNV Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility hide tableBrowser off - priority 0.5 + priority 2 #track me #shortLabel Regeneron Million Exomes 983k WES #longLabel SNV Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on #bigDataUrl /gbdb/$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 SNV Frequencies: NHLBI TOPMed - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_topmed/topmed10.vcf.gz dataVersion Freeze 10 tableBrowser off visibility hide - priority 2 + priority 22 track sfariSparkExomes shortLabel SFARI SPARK 140k WES longLabel SNV Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 tableBrowser off visibility hide - priority 2.5 + priority 26 track sfariSparkWgs shortLabel SFARI SPARK 12k WGS longLabel SNV Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 visibility hide - priority 2.5 + priority 25 html sfariSparkExomes tableBrowser off #track mcps #shortLabel Mexico City Prospective Study 10k WGS+141k WES #longLabel SNV Frequencies: Mexico City Prospective Study (MCPS) #tableBrowser off #parent varFreqs on #bigDataUrl /gbdb/$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 SNV Frequencies: Japan 61k - ToMMo SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility hide dataVersion 2025-06-16 - priority 5 + priority 17 track wbbc shortLabel China WBBC 4.5k WGS longLabel SNV Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz visibility hide dataVersion Phase I v20210103 - priority 5.5 + priority 6 track chinamap shortLabel China ChinaMAP 10.5k WGS longLabel SNV Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_chinamap/chinamap.vcf.gz visibility hide dataVersion Phase 1 (v2020-03.beta) - priority 5.55 + priority 5 tableBrowser off track tpmi shortLabel Taiwan TPMI Axiom array longLabel SNV Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz visibility hide dataVersion Axiom TPM1 2022-06 - priority 5.6 + priority 31 tableBrowser off track alfaVcf shortLabel NCBI ALFA 408k mixed 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 + priority 20 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 SNV Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS - priority 4.5 + priority 8 bigDataUrl /gbdb/$D/varFreqs/_finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track ukbb parent varFreqs on visibility hide type vcfTabix shortLabel UK Biobank 361k imputed longLabel SNV Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed - priority 4.6 + priority 32 bigDataUrl /gbdb/$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 SNV Frequencies: Sweden SweGen - 1k WGS - priority 4.7 + priority 30 bigDataUrl /gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track gonl parent varFreqs on visibility hide type vcfTabix shortLabel Netherlands GoNL 498 WGS longLabel SNV Frequencies: Genome of the Netherlands - 250 Dutch trios - priority 4.75 + priority 21 bigDataUrl /gbdb/$D/varFreqs/gonl/gonl.vcf.gz dataVersion GRCh38 1.0 track mgrb shortLabel Australia MGRB 4k WGS longLabel SNV Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 visibility hide + priority 3 # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia 1.7k SNVs longLabel SNV Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility hide + priority 11 dataVersion Pilot 2019 (lifted to hg38, May 2026) track gaspIndel shortLabel GenomeAsia 1.7k Indels longLabel SNV Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.indels.vcf.gz visibility hide + priority 10 dataVersion Pilot 2019 (lifted to hg38, May 2026) html gasp track abraom shortLabel Brazil ABraOM 1k WGS longLabel SNV Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility hide + priority 4 dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS longLabel SNV Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility hide + priority 16 dataVersion IndiGen pilot (Jain 2021) track genomeindia shortLabel India GenomeIndia 9.7k WGS longLabel SNV Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_genomeindia/genomeindia.vcf.gz tableBrowser off visibility hide dataVersion 9768GI_SummaryStats (Apr 2025) - priority 4.8 + priority 15 track kova shortLabel Korea KOVA 5.3k mixed longLabel SNV Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz visibility hide + priority 18 tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel SNV Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility hide + priority 28 tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS longLabel SNV Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz visibility hide + priority 14 dataVersion r1.1 track saudi shortLabel Saudi Genome 302 WGS longLabel SNV Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility hide + priority 23 dataVersion SHGP (figshare 51297884, 2025) track schema shortLabel SCHEMA 121k WES Sz longLabel SNV Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility hide dataVersion 2022 - priority 4.9 + priority 24 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track mxbFreq shortLabel Mexico Biobank 6k Array longLabel SNV Frequencies: Mexico Biobank - 6,011 individuals, genotyping array type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mxb/mxb.freq.vcf.gz visibility hide dataVersion Nov 2025 (hg38 lift) tableBrowser off - priority 6 + priority 19 track sgdpFreq shortLabel SGDP 279 WGS longLabel SNV Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility hide dataVersion 2016-12-07 (hg38 lift) - priority 7 + priority 27 track gregor shortLabel GREGoR R4 3.6k WGS longLabel SNV Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz visibility hide dataVersion R04 (Oct 2025) - priority 8 + priority 13 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS longLabel SNV Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz visibility hide dataVersion v3.1.2 - priority 8 + priority 12 track ga4kSnv shortLabel GA4K 552 PacBio LR longLabel SNV Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz visibility hide dataVersion Cohen 2022 release priority 9 track colorsDbSnv shortLabel CoLoRSdb 1k LR SNV/Ind longLabel SNV Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz visibility hide dataVersion v1.2.0 - priority 9.5 + priority 7 track svatalogSnv shortLabel SVatalog 101 WGS longLabel SNV Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz visibility hide dataVersion Chirmade 2025 release - priority 10 + priority 29 track tishkoff180 shortLabel 12 Afr Pops 180 WGS 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 + priority 1