aa8e2e87c3b54e9662d87cd5b921d5607fc846ad max Mon Nov 10 05:51:08 2025 -0800 adding korea to varFreqs supertrack, refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 82ab553b45d..3f374a06e12 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,93 +1,91 @@ track varFreqs shortLabel Variant Frequencies -longLabel Variant Frequencies from various population- or cohort-specific Projects +longLabel Variant Frequencies from various population-specific or national Projects group varRep type bed 12 visibility hide superTrack on track mexbb - shortLabel Mexico Biobank - longLabel Variant Frequencies: Mexico Biobank + shortLabel Mexico Biobank, 6k Array + longLabel Phased Variants: Mexico Biobank 6k Array tableBrowser off parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mexbb/MXBv2.vcf.gz visibility pack type vcfTabix hapClusterEnabled true - dataVersion Nov 2025 + dataVersion Nov 2025 (hg38 lift) priority 0.5 - track mcps - shortLabel Mexico City Prospective Study - longLabel Variant Frequencies: Mexico City Prospective Study (MCPS) - tableBrowser off - parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz - visibility pack - type vcfTabix - dataVersion May 2023 (v1.2.0) - priority 3 - track me - shortLabel Regeneron Million Exomes - longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project + shortLabel Regeneron Million Exomes 983k WES + longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS tableBrowser off parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz visibility pack type vcfTabix hapClusterEnabled true dataVersion 10/04/2023, v1.1.3 priority 1 track topmed - shortLabel NHLBI TOPMED 10 - longLabel Variant Frequencies: NHLBI TOPMED + shortLabel NHLBI TOPMED 10 151k WGS + longLabel Variant Frequencies: NHLBI TOPMED - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/topmed/topmed10.vcf.gz dataVersion Freeze 10 visibility pack priority 2 + 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/$D/varFreqs/mcps/mcps.freq.vcf.gz + visibility pack + type vcfTabix + dataVersion May 2023 (v1.2.0) + priority 3 + track tommo60kjpn - shortLabel Japan 61k ToMMO + shortLabel Japan ToMMO 61k WGS longLabel Variant Frequencies: Japan 61k - ToMMO SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility pack dataVersion 2025-06-16 priority 5 track ALFA compositeTrack on parent varFreqs on visibility pack itemRgb on type bigBed 9 + . - shortLabel NCBI ALFA - longLabel Variant Frequencies: NCBI ALFA (Allele Frequency Aggregator) from dbGaP + shortLabel NCBI ALFA 408k WGS/WES/array + longLabel Variant Frequencies: NCBI ALFA (Allele Frequency Aggregator) from dbGaP - 408k mixed WGS/WES/array mouseOverField frequency html ALFA.html filter.score 10 - #filterByRange.score on - #filterLimits.score 400:500 - #filterValues.name rs1424773263,rs2531320 priority 4 + dataVersion R4 track ALFA_GLB parent ALFA on shortLabel NCBI ALFA: Global bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_GLB.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_EUR parent ALFA on shortLabel NCBI ALFA: European bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_EUR.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab @@ -162,41 +160,85 @@ shortLabel NCBI ALFA: Latin American 2 bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_LEN.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_OTR parent ALFA on shortLabel NCBI ALFA: Other bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_OTR.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track hgdp - shortLabel Human Genome Diversity Project - longLabel Variant Frequencies: Human Genome Diversity Project (HGDP) - 1043 samples from indigenous and isolated populations + shortLabel Human Genome Diversity Project, 1k WGS + longLabel Phased Variants: Human Genome Diversity Project (HGDP) - 1043 samples, isolated populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp/hgdp_wgs.20190516.full.vcf.gz visibility pack dataVersion 2019-05-16 + priority 0.1 + + track sgdp + shortLabel Simons Genome Diversity Project 0.3k WGS + longLabel Phased Variants: Simons Genome Diversity Project - 279 samples, unmixed populations + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/sgdp/SGDP.nh2.vcf.gz + visibility pack + dataVersion 2016-12-07 public (hg38 lift) + priority 0.2 + + track hgdp1k + shortLabel gnomAD HGDP+1000G 4k WGS + longLabel Phased Variants: gnomAD HGDP + 1000 genomes callset - 4094 whole genomes, 80 populations + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/hgdp1k/hgdp1k.vcf.gz + visibility pack + dataVersion v 3.1.2 + priority 0.3 track gasp - shortLabel GenomeAsia Pilot Subs + shortLabel GenomeAsia Pilot Subs 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility pack - #dataVersion GAsP Pilot: 1,739 individuals track gaspIndel - shortLabel GenomeAsia Pilot Indels + shortLabel GenomeAsia Pilot Indels 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/All.indels.annot.cont_withmaf.vcf.gz visibility pack - #dataVersion GAsP Pilot: 1,739 individuals + + track abraom + shortLabel Brazil ABraOM 1k WGS + longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz + visibility pack + + track indigenomes + shortLabel India IndiGenomes 1k WGS + longLabel Variant Frequencies: IndiGenomes India - 1,029 samples + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz + visibility pack + + track kova + shortLabel Korea KOVA 1.9k WGS+3.5k WES + longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.5k WES + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/kova/kova.v7.vcf.gz + visibility pack + tableBrowser off