28bfc5e8e4301c0955eac938490458282438cf49 max Tue Nov 4 07:28:44 2025 -0800 adding HGDP and alfa docs page to var freqs track diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 56811e86168..82ab553b45d 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -4,165 +4,199 @@ group varRep type bed 12 visibility hide superTrack on track mexbb shortLabel Mexico Biobank longLabel Variant Frequencies: Mexico Biobank tableBrowser off parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mexbb/MXBv2.vcf.gz visibility pack type vcfTabix hapClusterEnabled true dataVersion Nov 2025 + priority 0.5 track mcps shortLabel Mexico City Prospective Study longLabel Variant Frequencies: Mexico City Prospective Study (MCPS) tableBrowser off parent varFreqs on bigDataUrl /gbdb/$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 tableBrowser off parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz visibility pack type vcfTabix hapClusterEnabled true dataVersion 10/04/2023, v1.1.3 + priority 1 track topmed shortLabel NHLBI TOPMED 10 longLabel Variant Frequencies: NHLBI TOPMED type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/topmed/topmed10.vcf.gz dataVersion Freeze 10 visibility pack + priority 2 - track gasp - shortLabel GenomeAsia Pilot Subs - longLabel Variant Frequencies: GenomeAsia Pilot Substitutions + track tommo60kjpn + shortLabel Japan 61k ToMMO + longLabel Variant Frequencies: Japan 61k - ToMMO SNV+Indels type vcfTabix parent varFreqs on - bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz + bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility pack - #dataVersion GAsP Pilot: 1,739 individuals + dataVersion 2025-06-16 + priority 5 track ALFA compositeTrack on - parent varFreqs + parent varFreqs on visibility pack itemRgb on type bigBed 9 + . shortLabel NCBI ALFA - longLabel NCBI ALFA: Allele Frequency Aggregator from dbGap submissions + longLabel Variant Frequencies: NCBI ALFA (Allele Frequency Aggregator) from dbGaP mouseOverField frequency html ALFA.html filter.score 10 #filterByRange.score on #filterLimits.score 400:500 #filterValues.name rs1424773263,rs2531320 + priority 4 track ALFA_GLB parent ALFA on shortLabel NCBI ALFA: Global - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_GLB.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_GLB.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_EUR parent ALFA on shortLabel NCBI ALFA: European - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_EUR.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_EUR.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_AFA parent ALFA on shortLabel NCBI ALFA: African American - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_AFA.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFA.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_AFO parent ALFA on shortLabel NCBI ALFA: African Others - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_AFO.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFO.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_AFR parent ALFA on shortLabel NCBI ALFA: African - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_AFR.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFR.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_EAS parent ALFA on shortLabel NCBI ALFA: East Asian - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_EAS.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_EAS.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_SAS parent ALFA on shortLabel NCBI ALFA: South Asian - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_SAS.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_SAS.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_OAS parent ALFA on shortLabel NCBI ALFA: Other Asian - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_OAS.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_OAS.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_ASN parent ALFA on shortLabel NCBI ALFA: Asian - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_ASN.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_ASN.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_LAC parent ALFA on shortLabel NCBI ALFA: Latin American 1 - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_LAC.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_LAC.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_LEN parent ALFA on shortLabel NCBI ALFA: Latin American 2 - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_LEN.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_LEN.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track ALFA_OTR parent ALFA on shortLabel NCBI ALFA: Other - bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_OTR.bb + bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_OTR.bb type bigBed 9 + . url https://www.ncbi.nlm.nih.gov/snp/$$#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 + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/hgdp/hgdp_wgs.20190516.full.vcf.gz + visibility pack + dataVersion 2019-05-16 + + track gasp + shortLabel GenomeAsia Pilot Subs + longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz + visibility pack + #dataVersion GAsP Pilot: 1,739 individuals + + track gaspIndel + shortLabel GenomeAsia Pilot Indels + 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 +