a21526733fec1b6e7930fae4758e1688aa125383 chmalee Tue Apr 23 10:30:40 2024 -0700 Removing test gnomad v3.1.1 track that was for QA testing only diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.ra src/hg/makeDb/trackDb/human/hg38/gnomad.ra index a21529b..dc8857a 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomad.ra +++ src/hg/makeDb/trackDb/human/hg38/gnomad.ra @@ -1,231 +1,195 @@ # Genome Aggregation Database # gnomad.broadinstitue.org track gnomadVariants superTrack on shortLabel gnomAD Variants longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants group varRep html gnomadV4 pennantIcon Updated red ../goldenPath/newsarch.html#032624 "Updated Mar. 26, 2024" track gnomadVariantsV2 parent gnomadVariants compositeTrack on shortLabel gnomAD v2 longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1 type vcfTabix showHardyWeinberg on configureByPopup off maxWindowToDraw 200000 pennantIcon 19.jpg ../goldenPath/help/liftOver.html "lifted from hg19" dataVersion Release 2.1.1 (March 6, 2019) html gnomadV3_1_1 priority 4 visibility hide track gnomadGenomesVariantsV2 parent gnomadVariantsV2 on shortLabel gnomAD Genome v2 longLabel Genome Aggregation Database (gnomAD) Genome Variants v2.1 bigDataUrl /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.gz priority 1 track gnomadExomesVariantsV2 parent gnomadVariantsV2 on shortLabel gnomAD Exome v2 longLabel Genome Aggregation Database (gnomAD) Exome Variants v2.1 bigDataUrl /gbdb/hg38/gnomAD/vcf/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz priority 2 track gnomadGenomesVariantsV3 parent gnomadVariants shortLabel gnomAD v3 longLabel Genome Aggregation Database (gnomAD) Genome Variants v3 dataVersion Release 3.0 (October 16, 2019) type vcfTabix showHardyWeinberg on configureByPopup off maxWindowToDraw 200000 html gnomad bigDataUrl /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r3.0.sites.vcf.gz priority 3 visibility hide url http://gnomad.broadinstitute.org/variant/$s-$<pos>-$<ref>-$<firstAlt>?dataset=gnomad_r3&ignore=$$ urlLabel gnomAD: track gnomadGenomesVariantsV3_1 parent gnomadVariants visibility hide shortLabel gnomAD v3.1 longLabel Genome Aggregation Database (gnomAD) Genome Variants v3.1 dataVersion Release 3.1 (October 29, 2020) type bigBed 9 + itemRgb on html gnomadV3_1_1 bigDataUrl /gbdb/hg38/gnomAD/v3.1/variants/genomes.bb priority 2 labelFields name,rsId defaultLabelFields name sepFields AC_afr filterValues.annot pLoF,missense,synonymous,other filterType.annot multiple filterValues.FILTER PASS,InbreedingCoeff,RF,AC0 filterType.FILTER multipleListAnd filterValuesDefault.FILTER PASS filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,TFBS_ablation,TF_binding_site_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intergenic_variant,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation filterType.variation_type multipleListOr filter.AF 0.0 filterLabel.AF Minor Allele Frequency Filter maxItems 50000 mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); Genes: $genes; Type: $annot; Tag: $FILTER; Allele Frequency: $AF ($AC/$AN) url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r3&ignore=$<rsId> urlLabel View this variant at gnomAD detailsStaticTable Population Frequencies|/gbdb/hg38/gnomAD/v3.1/variants/v3.1.genomes.popTable.txt - track gnomadV311Test - release alpha - bigDataUrl /hive/data/inside/gnomAD/v3.1.1/2024-02-12/genomes.bb - parent gnomadVariants - visibility squish - shortLabel TEST gnomAD v3.1.1 - longLabel TEST Genome Aggregation Database (gnomAD) Genome Variants v3.1.1 - dataVersion Release v3.1.1 (March 20, 2021) and v3.1 chrM Release (November 17, 2020) - type bigBed 9 + - itemRgb on - searchIndex name,_displayName,rsId - html gnomadV3_1_1 - priority 2 - labelFields rsId,_displayName - defaultLabelFields _displayName - skipFields _displayName - skipEmptyFields on - filterValues.AC_non_cancer Non-Cancer - filterValuesDefault.AC_non_cancer Non-Cancer - filterType.AC_non_cancer single - filterValues.annot pLoF,missense,synonymous,other - filterValuesDefault.annot pLoF,missense,synonymous - filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only) - filterType.FILTER multipleListAnd - filterValuesDefault.FILTER PASS - filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation - filterType.variation_type multipleListOr - filter.AF 0.0 - filterLabel.AF Minor Allele Frequency Filter - maxItems 50000 - mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); rsId: $rsId; Genes: $genes; Annotation: $annot; FILTER: $FILTER; Variation: $variation_type - url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r3&ignore=$<rsId> - urlLabel View this variant at gnomAD - detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies - detailsTabUrls _dataOffset=/hive/data/inside/gnomAD/v3.1.1/2024-02-12/gnomad.v3.1.1.details.tab.gz - track gnomadGenomesVariantsV3_1_1 parent gnomadVariants visibility squish shortLabel gnomAD v3.1.1 longLabel Genome Aggregation Database (gnomAD) Genome Variants v3.1.1 dataVersion Release v3.1.1 (March 20, 2021) and v3.1 chrM Release (November 17, 2020) type bigBed 9 + itemRgb on searchIndex name,_displayName,rsId html gnomadV3_1_1 bigDataUrl /gbdb/hg38/gnomAD/v3.1.1/genomes.bb priority 2 labelFields rsId,_displayName defaultLabelFields _displayName skipFields _displayName skipEmptyFields on filterValues.AC_non_cancer Non-Cancer filterValuesDefault.AC_non_cancer Non-Cancer filterType.AC_non_cancer single filterValues.annot pLoF,missense,synonymous,other filterValuesDefault.annot pLoF,missense,synonymous filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only) filterType.FILTER multipleListAnd filterValuesDefault.FILTER PASS filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation filterType.variation_type multipleListOr filter.AF 0.0 filterLabel.AF Minor Allele Frequency Filter maxItems 50000 mouseOver Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt); rsId: $rsId; Genes: $genes; Annotation: $annot; FILTER: $FILTER; Variation: $variation_type url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r3&ignore=$<rsId> urlLabel View this variant at gnomAD detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v3.1.1/gnomad.v3.1.1.details.tab.gz pennantIcon Updated red ../goldenPath/newsarch.html#032624 "Updated Mar. 26, 2024" track gnomadConstraint parent gnomadVariants on shortLabel gnomAD Mut Constraint longLabel Genome Aggregation Database (gnomAD) non-coding constraint of haploinsufficient variation (Gnocchi), includes chrX bigDataUrl /gbdb/hg38/gnomAD/mutConstraint/mutConstraint.bw type bigWig altColor 0,150,0 color 150,0,0 maxHeightPixels 128:40:8 viewLimitsMax -3:3 autoScale on priority 10 dataVersion Release 3.1.2 (October 22, 2021) html gnomadV3_1_1 # The missense and pLI contraint tracks include gnomad.constraint.public.ra track gnomadVariantsV4 parent gnomadVariants compositeTrack on shortLabel gnomAD v4 Pre-Release longLabel Genome Aggregation Database (gnomAD) Genome Variants v4.0.0 Pre-Release type vcfTabix showHardyWeinberg on configureByPopup off visibility dense dataVersion Release 4.0.0 (November 1, 2023, (chrY Fix November 16, 2023)) priority 1 url http://gnomad.broadinstitute.org/variant/$s-$<pos>-$<ref>-$<firstAlt>?dataset=gnomad_r4&ignore=$$ urlLabel gnomAD: html gnomadV4.html track gnomadGenomesV4 parent gnomadVariantsV4 chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY shortLabel gnomAD4 Genome Vars longLabel Genome Aggregation Database (gnomAD) Genomes Variants v4.0.0 Pre-Release maxWindowCoverage 1000 maxWindowToDraw 10000 visibility pack track gnomadExomesV4 parent gnomadVariantsV4 chromosomes chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chrX,chrY shortLabel gnomAD4 Exome Vars longLabel Genome Aggregation Database (gnomAD) Exomes Variants v4.0.0 Pre-Release visibility pack maxWindowCoverage 1000 maxWindowToDraw 10000 searchTable pliByTranscript searchType bigBed searchDescription gnomAD Loss of Function Metrics by Transcript searchTable pliByGene searchType bigBed searchDescription gnomAD Loss of Function Metrics by Gene searchName gnomadGenomesVariantsV3_1_1_displayName searchTable gnomadGenomesVariantsV3_1_1 searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Genome Variants v3.1.1 termRegex ^chr([1-9][0-9]?|[XYM]):[0-9]+-[0-9]+-* searchName gnomadGenomesVariantsV3_1_1_rsId searchTable gnomadGenomesVariantsV3_1_1 searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Genome Variants v3.1.1 termRegex ^rs* searchTable gnomadGenomesVariantsV3_1_1_name searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Genome Variants v3.1.1