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 Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt)
rsId: $rsId
Genes: $genes
Annotation: $annot
FILTER: $FILTER
Var type: $variation_type
url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$[-$?dataset=gnomad_r3&ignore=$
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 Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt)]
TotalAF: ${AF} (${AC}/${AN})
Genes: $genes
Annotation: $annot
FILTER: ${FILTER}
PopMaxAF: ${grpmax}
Homozygous Individuals: ${nhomalt}
Hemizygous Individuals (only in chrX & chrY): ${nhemi}
- url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$[-$?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 Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt)]
TotalAF: ${AF} (${AC}/${AN})
Genes: $genes
Annotation: $annot
FILTER: ${FILTER}
PopMaxAF: ${grpmax}
Homozygous Individuals: ${nhomalt}
Hemizygous Individuals (only in chrX & chrY): ${nhemi}
- url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$[-$?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 Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt)]
TotalAF: ${AF} (${AC}/${AN})
Genes: $genes
Annotation: $annot
FILTER: ${FILTER}
PopMaxAF: ${grpmax}
Homozygous Individuals: ${nhomalt}
Hemizygous Individuals (only in chrX & chrY): ${nhemi}
url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$[-$?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 Position: $chrom:${chromStart}-${chromEnd} ($ref/$alt)]
TotalAF: ${AF} (${AC}/${AN})
Genes: $genes
Annotation: $annot
FILTER: ${FILTER}
PopMaxAF: ${grpmax}
Homozygous Individuals: ${nhomalt}
Hemizygous Individuals (only in chrX & chrY): ${nhemi}
url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$[-$?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
]