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 = () => {
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"), },