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Annotate NMD-triggering/skipping nonsense variants through the VEP plugin: http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#nmd
The text was updated successfully, but these errors were encountered:
This will imply two steps:
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Change the way we run VEP in the Intogen pipeline step that prepares the datasets for boostDM.
I am currently working on this step to include it in a patch from IntOGen 2024.
The new vep.tsv.gz is located here: /workspace/projects/intogen_plus/containers/datasets_patch_24_11/boostdm/
/workspace/projects/intogen_plus/containers/datasets_patch_24_11/boostdm/
The file looks like this:
1 65565 A C ENSG00000186092 ENST00000641515 Transcript start_lost 61 1 1 M/L Atg/Ctg - HIGH- 1 - OR4F5 HGNC HGNC:14825 YES NM_001005484.2 - ENSP00000493376 2/3 - -
where the last column is the NMD one. The unique values are the following:
❯ zcat vep.tsv.gz | cut -f 28 | grep -v "-" | sort -u NMD_escaping_variant -
FedericaBrando
Successfully merging a pull request may close this issue.
Annotate NMD-triggering/skipping nonsense variants through the VEP plugin:
http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#nmd
The text was updated successfully, but these errors were encountered: