a35bd5603343fd35129bca74f979310e4368dd13 max Mon Dec 1 08:09:21 2025 -0800 fixing tdb error diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index e534a0d9fdd..0299f1b7664 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,235 +1,234 @@ track varFreqs shortLabel Variant Frequencies longLabel Variant Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on track me shortLabel Regeneron Million Exomes 983k WES longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz visibility pack type vcfTabix hapClusterEnabled true dataVersion 10/04/2023, v1.1.3 tableBrowser off priority 1 track allofus shortLabel AllOfUs v7 245k WGS longLabel Variant Frequencies: AllOfUs - v7 245k WGS - BROKEN AFTER CHR8 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 finngen parent varFreqs on visibility pack - itemRgb on type vcfTabix shortLabel Finngen longLabel Variant Frequencies: Finnland Finngen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track gasp shortLabel GenomeAsia Pilot Subs 1.7k WGS longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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 dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel Variant Frequencies: NPM Singapore - 9,770 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility pack tableBrowser off dataVersion r5.3.2