172029e2893855d715acbfb8c69f30380a5c45ac max Fri Nov 14 08:34:01 2025 -0800 creating phased variants track,refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 4988c6def8a..80b9a69a942 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,255 +1,213 @@ track varFreqs -shortLabel Variants of the World -longLabel Variant Frequencies from various population-specific or national Projects +shortLabel Variant Frequencies +longLabel Variant Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on - track mexbb - shortLabel Mexico Biobank, 6k Array - longLabel Phased Variants: Mexico Biobank 6k Array - tableBrowser off - parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/mexbb/MXBv2.vcf.gz - visibility pack - type vcfTabix - hapClusterEnabled true - dataVersion Nov 2025 (hg38 lift) - priority 0.5 - track me shortLabel Regeneron Million Exomes 983k WES longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS tableBrowser off parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz visibility pack type vcfTabix hapClusterEnabled true dataVersion 10/04/2023, v1.1.3 + tableBrowser off priority 1 track allofus shortLabel AllOfUs v7 245k WGS longLabel Variant Frequencies: AllOfUs - v7 245k WGS - BROKEN AFTER CHR8 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/allofus/allOfUs.locAncFreq.sort.vcf.gz dataVersion V7 visibility pack priority 2.5 - track topmed shortLabel NHLBI TOPMED 10 151k WGS longLabel Variant Frequencies: NHLBI TOPMED - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/topmed/topmed10.vcf.gz dataVersion Freeze 10 visibility 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/$D/varFreqs/mcps/mcps.freq.vcf.gz visibility pack type vcfTabix dataVersion May 2023 (v1.2.0) priority 3 track tommo60kjpn shortLabel Japan ToMMO 61k WGS longLabel Variant Frequencies: Japan 61k - ToMMO SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 408k WGS/WES/array longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array mouseOverField frequency html ALFA.html filter.score 10 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 urlLabel NCBI Variation Page track ALFA_AFA parent ALFA on shortLabel NCBI ALFA: African American bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFA.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_AFO parent ALFA on shortLabel NCBI ALFA: African Others bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFO.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_AFR parent ALFA on shortLabel NCBI ALFA: African bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFR.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_EAS parent ALFA on shortLabel NCBI ALFA: East Asian bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_EAS.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_SAS parent ALFA on shortLabel NCBI ALFA: South Asian bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_SAS.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_OAS parent ALFA on shortLabel NCBI ALFA: Other Asian bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_OAS.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_ASN parent ALFA on shortLabel NCBI ALFA: Asian bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_ASN.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_LAC parent ALFA on shortLabel NCBI ALFA: Latin American 1 bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_LAC.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_LEN parent ALFA on 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, 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/$D/varFreqs/hgdp1k/hgdp1k.vcf.gz - visibility pack - dataVersion v 3.1.2 - priority 0.3 - track gasp shortLabel GenomeAsia Pilot Subs 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility pack track gaspIndel shortLabel GenomeAsia Pilot Indels 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/All.indels.annot.cont_withmaf.vcf.gz visibility pack track abraom shortLabel Brazil ABraOM 1k WGS longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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