4f8f8773bec66a9e993e9897e0b032c6e97dead8 max Fri May 15 10:12:29 2026 -0700 mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 021c4d2f18c..923573b25d4 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -271,74 +271,78 @@ filterLabel.NPMAC_Chinese NPM Singapore Chinese AC filterByRange.NPMAC_Malay on filterLabel.NPMAC_Malay NPM Singapore Malay AC filterByRange.NPMAC_Indian on filterLabel.NPMAC_Indian NPM Singapore Indian AC skipEmptyFields on track allofus shortLabel AllOfUs v7 245k WGS longLabel Variant Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility dense + 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 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/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 visibility dense + tableBrowser off priority 2.5 track sfariSparkWgs shortLabel SFARI SPARK 12k WGS longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz 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/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) #priority 3 track tommo60kjpn shortLabel Japan ToMMo 61k WGS longLabel Variant Frequencies: Japan 61k - ToMMo SNV+Indels @@ -347,62 +351,72 @@ bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility dense 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 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 + visibility dense + dataVersion Axiom TPM1 2022-06 + priority 5.6 + 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/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track ukbb parent varFreqs on visibility dense type vcfTabix shortLabel UK Biobank 361k imputed - longLabel Variant Frequencies: UK Biobank - 361k White British, Neale Lab Round 2 imputed + longLabel Variant Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed priority 4.6 bigDataUrl /gbdb/$D/varFreqs/ukbb/ukbb.vcf.gz - dataVersion Neale Lab Round 2 (Aug 2018, hg19 lift) + 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/$D/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track mgrb shortLabel Australia MGRB 4k WGS longLabel Variant Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS @@ -497,60 +511,61 @@ bigDataUrl /gbdb/$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/$D/varFreqs/mxb/mxb.freq.vcf.gz visibility dense dataVersion Nov 2025 (hg38 lift) + tableBrowser off priority 6 track sgdpFreq shortLabel SGDP 279 WGS longLabel Variant Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility dense dataVersion 2016-12-07 (hg38 lift) priority 7 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/$D/varFreqs/gregor/gregor.vcf.gz visibility dense dataVersion R04 (Oct 2025) priority 8 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS longLabel Variant Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz visibility dense - dataVersion v3.1.2 + dataVersion gnomAD 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 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