10db3769dd9edfa38ac8d900ca400fdfb514d9a7 gperez2 Wed Jul 29 22:41:46 2026 -0700 An in-place update for gnomad v4.1 to v4.1.1 that swaps bigDataUrl, labels, dataVersion, detailsTabUrls, search descriptions, and removes the alpha-only gnomadVariantsV4.1.1 composite. Updates to gnomad.html, gnomadV4.1.html, and gnomadPLI.html regarding the addition of the gnomad v4.1.1 data, refs #37351 diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.ra src/hg/makeDb/trackDb/human/hg38/gnomad.ra index 463f31bfb51..e181c49c615 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomad.ra +++ src/hg/makeDb/trackDb/human/hg38/gnomad.ra @@ -110,181 +110,102 @@ 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 + shortLabel gnomAD v4.1.1 + longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1.1 type bigBed 9 + configureByPopup off maxWindowCoverage 200000 maxItems 50000 - dataVersion Release v4.1 (April 19, 2024) + dataVersion Release v4.1.1 (March 30, 2026) 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 gnomadVariantsV4.1.1 - parent gnomadVariants - compositeTrack on - shortLabel gnomAD v4.1.1 - longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1.1 - type bigBed 9 + - configureByPopup off - maxWindowCoverage 200000 - maxItems 50000 - dataVersion Release v4.1.1 - html gnomadV4.1 - priority 0.5 - visibility squish - release alpha - - track gnomadExomesVariantsV4_1_1 - parent gnomadVariantsV4.1.1 on - visibility squish shortLabel gnomAD v4.1.1 Exomes longLabel Genome Aggregation Database (gnomAD) Exomes Variants v4.1.1 - dataVersion Release v4.1.1 + dataVersion Release v4.1.1 (March 30, 2026) type bigBed 9 + itemRgb on searchIndex name,_displayName,rsId html gnomadV4.1 bigDataUrl /gbdb/hg38/gnomAD/v4.1.1/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/v4.1.1/exomes/gnomad.v4.1.1.exomes.details.tab.gz - release alpha - track gnomadGenomesVariantsV4_1_1 - parent gnomadVariantsV4.1.1 on + track gnomadGenomesVariantsV4_1 + parent gnomadVariantsV4.1 on visibility squish shortLabel gnomAD v4.1.1 Genomes longLabel Genome Aggregation Database (gnomAD) Genome Variants v4.1.1 - dataVersion Release v4.1.1 + dataVersion Release v4.1.1 (March 30, 2026) type bigBed 9 + itemRgb on searchIndex name,_displayName,rsId html gnomadV4.1 bigDataUrl /gbdb/hg38/gnomAD/v4.1.1/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/v4.1.1/genomes/gnomad.v4.1.1.genomes.details.tab.gz - release alpha 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 @@ -377,75 +298,43 @@ 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 +searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1.1 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 +searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1.1 termRegex ^rs* searchTable gnomadGenomesVariantsV4_1_name searchType bigBed -searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1 +searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1.1 searchName gnomadExomesVariantsV4_1_displayName searchTable gnomadExomesVariantsV4_1 searchType bigBed -searchDescription Genome Aggregation Database (gnomAD) Exomes Variants v4.1 +searchDescription Genome Aggregation Database (gnomAD) Exomes Variants v4.1.1 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 - -searchName gnomadGenomesVariantsV4_1_1_displayName -searchTable gnomadGenomesVariantsV4_1_1 -searchType bigBed -searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1.1 -termRegex ^chr([1-9][0-9]?|[XYM])-[0-9]+-.* - -searchName gnomadGenomesVariantsV4_1_1_rsId -searchTable gnomadGenomesVariantsV4_1_1 -searchType bigBed -searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1.1 -termRegex ^rs* - -searchTable gnomadGenomesVariantsV4_1_1_name -searchType bigBed -searchDescription Genome Aggregation Database (gnomAD) Genome Variants v4.1.1 - -searchName gnomadExomesVariantsV4_1_1_displayName -searchTable gnomadExomesVariantsV4_1_1 -searchType bigBed -searchDescription Genome Aggregation Database (gnomAD) Exomes Variants v4.1.1 -termRegex ^chr([1-9][0-9]?|[XYM])-[0-9]+-.* - -searchName gnomadExomesVariantsV4_1_1_rsId -searchTable gnomadExomesVariantsV4_1_1 -searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Exomes Variants v4.1.1 termRegex ^rs* -searchTable gnomadExomesVariantsV4_1_1_name +searchTable gnomadExomesVariantsV4_1_name searchType bigBed searchDescription Genome Aggregation Database (gnomAD) Exomes Variants v4.1.1