90668959b76ef7d792bac3cbc4eb509a58c6c317 chmalee Thu Apr 23 11:25:38 2026 -0700 Adding mergeSpannedItems to gnomad CNV and structural variants tracks on hg38, refs Max email diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.ra src/hg/makeDb/trackDb/human/hg38/gnomad.ra index 2cad32187f0..97a6eb2c45c 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomad.ra +++ src/hg/makeDb/trackDb/human/hg38/gnomad.ra @@ -1,337 +1,339 @@ # Genome Aggregation Database # gnomad.broadinstitue.org track gnomadVariants superTrack on shortLabel gnomAD longLabel Genome Aggregation Database (gnomAD) group varRep cartVersion 6 pennantIcon New red ../goldenPath/newsarch.html#041026 "New gnomAD STR track added Apr. 10, 2026" html gnomad 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) priority 4 visibility hide html gnomadV2.html 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 bigDataUrl /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r3.0.sites.vcf.gz priority 3.3 visibility hide url http://gnomad.broadinstitute.org/variant/$s-$<pos>-$<ref>-$<firstAlt>?dataset=gnomad_r3&ignore=$$ urlLabel gnomAD: html gnomadV3.html track gnomadGenomesVariantsV3_1 parent gnomadVariants visibility hide shortLabel Deprecated: gnomAD v3.1 longLabel Deprecated: Genome Aggregation Database (gnomAD) Genome Variants v3.1 dataVersion Release 3.1 (October 29, 2020) type bigBed 9 + itemRgb on bigDataUrl /gbdb/hg38/gnomAD/v3.1/variants/genomes.bb priority 3.2 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 <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>rsId</b>: $rsId<br> <b>Genes</b>: $genes<br> <b>Type</b>: $annot<br> <b>Tag</b>: $FILTER<br> <b>Allele Frequency</b>: $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 html gnomadV3.html track gnomadGenomesVariantsV3_1_1 parent gnomadVariants visibility hide 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 bigDataUrl /gbdb/hg38/gnomAD/v3.1.1/genomes.bb priority 3.1 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 <b>Position</b>: $chrom:${chromStart}-${chromEnd}} ($ref/$alt)<br> <b>rsId</b>: $rsId<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: $FILTER<br> <b>Var type</b>: $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 html gnomadV3.html track gnomadVariantsV4.1 parent gnomadVariants compositeTrack on shortLabel gnomAD v4.1 longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1 type bigBed 9 + configureByPopup off maxWindowCoverage 200000 maxItems 50000 dataVersion Release v4.1 (April 19, 2024) html gnomadV4.1 priority 1 visibility squish track gnomadExomesVariantsV4_1 parent gnomadVariantsV4.1 on visibility squish shortLabel gnomAD v4.1 Exomes longLabel Genome Aggregation Database (gnomAD) Exomes Variants v4.1 dataVersion Release v4.1 (April 19, 2024) type bigBed 9 + itemRgb on searchIndex name,_displayName,rsId html gnomadV4.1 bigDataUrl /gbdb/hg38/gnomAD/v4.1/exomes/exomes.bb priority 2 labelFields rsId,_displayName defaultLabelFields _displayName skipFields _displayName skipEmptyFields on 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 mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>TotalAF</b>: ${AF} (${AC}/${AN})<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: ${FILTER}<br> <b>PopMaxAF</b>: ${grpmax}<br> <b>Homozygous Individuals</b>: ${nhomalt}<br> <b>Hemizygous Individuals (only in chrX & chrY)</b>: ${nhemi} url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r4 urlLabel View this variant at gnomAD detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1/exomes/gnomad.v4.1.exomes.details.tab.gz track gnomadGenomesVariantsV4_1 parent gnomadVariantsV4.1 on visibility squish shortLabel gnomAD v4.1 Genomes longLabel Genome Aggregation Database (gnomAD) Genome Variants v4.1 dataVersion Release v4.1 (April 19, 2024) type bigBed 9 + itemRgb on searchIndex name,_displayName,rsId html gnomadV4.1 bigDataUrl /gbdb/hg38/gnomAD/v4.1/genomes/genomes.bb priority 1 labelFields rsId,_displayName defaultLabelFields _displayName skipFields _displayName skipEmptyFields on 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 mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>TotalAF</b>: ${AF} (${AC}/${AN})<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: ${FILTER}<br> <b>PopMaxAF</b>: ${grpmax}<br> <b>Homozygous Individuals</b>: ${nhomalt}<br> <b>Hemizygous Individuals (only in chrX & chrY)</b>: ${nhemi} url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r4 urlLabel View this variant at gnomAD detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1/genomes/gnomad.v4.1.genomes.details.tab.gz track gnomadConstraint parent gnomadVariants on shortLabel gnomAD Mut Constraint longLabel Gnocchi: Genome Aggregation Database (gnomAD) non-coding constraint of haploinsufficient variation, includes chrX bigDataUrl /gbdb/hg38/gnomAD/mutConstraint/mutConstraint.bw type bigWig setColorWith /gbdb/hg38/gnomAD/mutConstraint/mutConstraint.color.bb windowingFunction minimum 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 gnomadConstraint # The missense and pLI contraint tracks include gnomad.constraint.public.ra include gnomadCoverage.ra track gnomadStructuralVariants parent gnomadVariants on bigDataUrl /gbdb/hg38/gnomAD/v4/structuralVariants/gnomad.v4.1.sv.non_neuro_controls.sites.bb shortLabel gnomAD Structural Variants longLabel Genome Aggregation Database (gnomAD) - Structural Variants v4.1 dataVersion Release 4.1 (November 01, 2023) type bigBed 9 + itemRgb on visibility hide url https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_sv_r4 urlLabel gnomAD Structural Variant Browser filter.af_non_neuro 0:1 filterByRange.af_non_neuro on filterLimits.af_non_neuro 0:1 filterLabel.af_non_neuro Filter by non-neurological allele frequency filter.af_controls 0:1 filterByRange.af_controls on filterLimits.af_controls 0:1 filterLabel.af_controls Filter by common disease control allele frequency filterLabel.svtype Type of Variation filterValues.svtype BND|Breakend,CPX|Complex,CTX|Translocation,DEL|Deletion,DUP|Duplication,INS|Insertion,INV|Inversion,MCNV|Multi-allele CNV filter.svlen 50:199840172 filterByRange.svlen on filterLabel.svlen Filter by Variant Size mouseOverField _mouseOver filterValues.FILTER PASS,HIGH_NCR,IGH_MHC_OVERLAP,UNRESOLVED,REFERENCE_ARTIFACT filterValuesDefault.FILTER PASS filterType.FILTER multipleListAnd html gnomadSv.html +mergeSpannedItems on track gnomadCopyNumberVariants parent gnomadVariants on bigDataUrl /gbdb/hg38/gnomAD/v4/cnv/gnomad.v4.1.cnv.all.bb shortLabel gnomAD Rare CNV Variants longLabel Genome Aggregation Database (gnomAD) - Rare CNV variants (<1% overall site frequency) v4.1 dataVersion Release 4.1 (November 01, 2023) type bigBed 9 + itemRgb on visibility hide url https://gnomad.broadinstitute.org/variant/$$?dataset=gnomad_cnv_r4 urlLabel gnomAD Copy number variants Browser filterLabel.svtype Type of Variation filterValues.svtype DEL|Deletion,DUP|Duplication searchIndex name mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd}<br> <b>Size of variant</b>: ${svlen}<br> <b>Genes impacted by variant</b>: ${genes}<br> <b>Site frequency (non-neuro control samples)</b>: ${sf} html gnomadCNV +mergeSpannedItems on track gnomadStr parent gnomadVariants on shortLabel gnomAD STR longLabel Genome Aggregation Database (gnomAD) - Short Tandem Repeat Genotypes at Disease-Associated Loci pennantIcon New red ../goldenPath/newsarch.html#041026 "Released Apr. 10, 2026" dataVersion gnomAD v3.1.3 STR genotypes (March 2025) type bigBed 9 + itemRgb on bigDataUrl /gbdb/hg38/gnomAD/gnomadStr.bb visibility pack url https://gnomad.broadinstitute.org/short-tandem-repeat/$$?dataset=gnomad_r3 urlLabel View at gnomAD searchIndex name mouseOver <b>Gene:</b> $gene<br> <b>Repeat Motif(s):</b> $motif<br> <b>Number of samples:</b> $nSamples <br> <b>Passing quality filter:</b> $nPass <br> <b>Population sample counts:</b> $populations html gnomadStr 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]+-.* 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 searchName gnomadGenomesVariantsV4_1_displayName searchTable gnomadGenomesVariantsV4_1 searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1 termRegex ^chr([1-9][0-9]?|[XYM])-[0-9]+-.* searchName gnomadGenomesVariantsV4_1_rsId searchTable gnomadGenomesVariantsV4_1 searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1 termRegex ^rs* searchTable gnomadGenomesVariantsV4_1_name searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1 searchName gnomadExomesVariantsV4_1_displayName searchTable gnomadExomesVariantsV4_1 searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Exomes Variants v4.1 termRegex ^chr([1-9][0-9]?|[XYM])-[0-9]+-.* searchName gnomadExomesVariantsV4_1_rsId searchTable gnomadExomesVariantsV4_1 searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Exomes Variants v4.1 termRegex ^rs* searchTable gnomadExomesVariantsV4_1_name searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Exomes Variants v4.1