diff --git a/browser/help/topics/v4-browser-hts.md b/browser/help/topics/v4-browser-hts.md index 61dd76253..0ba3a287c 100644 --- a/browser/help/topics/v4-browser-hts.md +++ b/browser/help/topics/v4-browser-hts.md @@ -182,12 +182,15 @@ Row fields: - `xstart`: Transcript genomic start position (format: chromosomeposition). - `xstop`: Transcript genomic stop position (format: chromosomeposition). - `exons`: Array containing transcript exon information. - - `feature_type`: Exon type (e.g., CDS). - - `start`: Exon genomic start position (position only). - - `stop`: Exon genomic stop position (position only). - - `xstart`: Exon genomic start position (format: chromosomeposition). - - `xstop`: Exon genomic start position (format: chromosomeposition). + - `feature_type`: Exon type (e.g., CDS). + - `start`: Exon genomic start position (position only). + - `stop`: Exon genomic stop position (position only). + - `xstart`: Exon genomic start position (format: chromosomeposition). + - `xstop`: Exon genomic start position (format: chromosomeposition). - `reference_genome`: Reference genome associated with this transcript. + - `gtex_tissue_expression`: Array containing [GTEx](https://gtexportal.org/home/) v10 information. + - `tissue`: The tissue type, e.g. 'brain_cerebellum'. + - `value`: The Transript Per Million (TPM) value associated with the tissue. - `refseq_id`: Transcript RefSeq ID. - `refseq_version`: RefSeq version. - `hgnc_id`: HGNC gene ID. @@ -208,6 +211,15 @@ Row fields: - `ensembl_version`: Ensembl version. - `refseq_id`: Transcript RefSeq ID. - `refseq_version`: RefSeq version. +- `pext`: Struct containing [pext](https://gnomad.broadinstitute.org/help/pext) information. + - `regions`: Array containing pext information by region. + - `chrom`: The chromosome in which the region is located. + - `start`: Region genomic start position (position only). + - `stop`: Region genomic stop position (position only). + - `mean`: Mean expression across all tissues for the region. + - `tissues`: Array containing tissue information. + - `tissue`: The tissue type, e.g. 'brain_cerebellum'. + - `value`: The pext score for the tissue in the region. - `preferred_transcript_id`: Transcript shown on the gene page by default. Field contains MANE Select transcript ID if it exists, otherwise contains Ensembl canonical transcript ID. - `preferred_transcript_source`: Source of transcript ID used for `preferred_transcript_id` field; either "`mane_select`" or "`ensembl_canonical`". - `gnomad_constraint`: Struct containing gnomAD constraint information for gene. Struct is only present on the GRCh37 Hail Table. diff --git a/browser/src/DataPage/GnomadV2Downloads.tsx b/browser/src/DataPage/GnomadV2Downloads.tsx index 524d1e902..e060482b3 100644 --- a/browser/src/DataPage/GnomadV2Downloads.tsx +++ b/browser/src/DataPage/GnomadV2Downloads.tsx @@ -303,7 +303,7 @@ const GnomadV2Downloads = () => { diff --git a/browser/src/DataPage/GnomadV4Downloads.tsx b/browser/src/DataPage/GnomadV4Downloads.tsx index 06104295a..c78957a54 100644 --- a/browser/src/DataPage/GnomadV4Downloads.tsx +++ b/browser/src/DataPage/GnomadV4Downloads.tsx @@ -293,7 +293,7 @@ const GnomadV4Downloads = () => { diff --git a/browser/src/GenePage/GenePage.tsx b/browser/src/GenePage/GenePage.tsx index f93a8712b..ad5cca082 100644 --- a/browser/src/GenePage/GenePage.tsx +++ b/browser/src/GenePage/GenePage.tsx @@ -574,6 +574,7 @@ const GenePage = ({ datasetId, gene, geneId }: Props) => { includeNonCodingTranscripts={includeNonCodingTranscripts} includeUTRs={includeUTRs} zoomRegion={zoomRegion} + hasOnlyNonCodingTranscripts={!hasCodingExons && hasNonCodingTranscripts} /> )} diff --git a/browser/src/GenePage/VariantsInGene.tsx b/browser/src/GenePage/VariantsInGene.tsx index da367cf91..ebff5cadc 100644 --- a/browser/src/GenePage/VariantsInGene.tsx +++ b/browser/src/GenePage/VariantsInGene.tsx @@ -82,6 +82,7 @@ type OwnVariantsInGeneProps = { start: number stop: number } + hasOnlyNonCodingTranscripts?: boolean } // @ts-expect-error TS(2456) FIXME: Type alias 'VariantsInGeneProps' circularly refere... Remove this comment to see the full error message @@ -97,6 +98,7 @@ const VariantsInGene = ({ includeUTRs, variants, zoomRegion, + hasOnlyNonCodingTranscripts, }: VariantsInGeneProps) => { const datasetLabel = labelForDataset(datasetId) @@ -134,9 +136,12 @@ const VariantsInGene = ({ {includeNonCodingTranscripts || includeUTRs ? 'Warning' : 'Note'} {' '} - Only variants located in or within 75 base pairs of a coding exon are shown here. To see - variants in UTRs or introns, use the{' '} - region view. + {hasOnlyNonCodingTranscripts && <>This gene has no coding transcripts. } + Only variants located in or within 75 base pairs of{' '} + {!hasOnlyNonCodingTranscripts ? <>a coding exon (CDS) : <>an exon} are shown here. + To see variants {!hasOnlyNonCodingTranscripts ? <>in UTRs or introns : <>in introns} + , use the region view + .

The table below shows the HGVS consequence and VEP annotation for each variant's most diff --git a/data-pipeline/src/data_pipeline/data_types/gene.py b/data-pipeline/src/data_pipeline/data_types/gene.py index f6221afb5..cfa469b19 100644 --- a/data-pipeline/src/data_pipeline/data_types/gene.py +++ b/data-pipeline/src/data_pipeline/data_types/gene.py @@ -234,7 +234,7 @@ def prepare_gene_table_for_release(genes_path, keep_mane_version_global_annotati else: ds = ds.select_globals() - ds = ds.repartition(50) + ds = ds.repartition(100) return ds diff --git a/data-pipeline/src/data_pipeline/pipelines/genes.py b/data-pipeline/src/data_pipeline/pipelines/genes.py index 7b7ab14eb..96ed9e156 100644 --- a/data-pipeline/src/data_pipeline/pipelines/genes.py +++ b/data-pipeline/src/data_pipeline/pipelines/genes.py @@ -401,7 +401,7 @@ def annotate_with_preferred_transcript(table_path): pipeline.add_task( "prepare_grch37_genes_table_for_public_release", prepare_gene_table_for_release, - f"/{genes_subdir}/gnomad.browser.GRCh37.GENCODEv19.ht", + f"/{genes_subdir}/gnomad.browser.GRCh37.GENCODEv19.pext.ht", { "genes_path": pipeline.get_task("annotate_grch37_genes_step_5"), }, @@ -489,7 +489,7 @@ def annotate_with_constraint(genes_path, constraint_path): pipeline.add_task( "prepare_grch38_genes_table_for_public_release", prepare_gene_table_for_release, - f"/{genes_subdir}/gnomad.browser.GRCh38.GENCODEv39.ht", + f"/{genes_subdir}/gnomad.browser.GRCh38.GENCODEv39.pext.ht", { "genes_path": pipeline.get_task("remove_grch38_genes_constraint_for_release"), },