598adc82015a64774f87a3cd2d6a97e77906544b max Thu Jan 8 08:13:11 2026 -0800 adding SFARI SPARK WES to variant frequencies track, refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index b4ab2509e6f..d09171e5d10 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,252 +1,263 @@ track varFreqs shortLabel Variant Frequencies longLabel Variant Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on track allofus shortLabel AllOfUs v7 245k WGS - longLabel Variant Frequencies: AllOfUs - v7 245k WGS + longLabel Variant Frequencies: AllOfUs - v7 245k WGS, only with allele count >= 20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility pack priority 0.5 track me shortLabel Regeneron Million Exomes 983k WES longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.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/$D/varFreqs/topmed/topmed10.vcf.gz dataVersion Freeze 10 visibility pack priority 2 + track sfariSparkExomes + shortLabel SFARI Spark 140k WES + longLabel Variant Frequencies: SFARI SPARK - 140k WES + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.sites.vcf.gz + dataVersion iWES v3 2024_08 + visibility pack + priority 2.5 + 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 type vcfTabix shortLabel Finnland Finngen 500k imputed longLabel Variant Frequencies: Finnland Finngen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track swefreq parent varFreqs on visibility pack type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel Variant Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$D/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 + tableBrowser off track 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/$D/varFreqs/abraom/abraom.vcf.gz visibility pack dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS longLabel Variant Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$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/$D/varFreqs/kova/kova.v7.vcf.gz visibility pack tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility pack tableBrowser off dataVersion r5.3.2 track saudi shortLabel Saudi Genome Project 302 WGS longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility pack