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Update NMD rule #16

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koszulordie opened this issue Aug 2, 2024 · 3 comments · May be fixed by #26
Open

Update NMD rule #16

koszulordie opened this issue Aug 2, 2024 · 3 comments · May be fixed by #26
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@koszulordie
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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

@koszulordie
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This will imply two steps:

  • Change the way we run VEP in the Intogen pipeline step that prepares the datasets for boostDM.
  • Modify the scripts in boostDM accordingly.

@FedericaBrando FedericaBrando self-assigned this Nov 27, 2024
@FedericaBrando FedericaBrando added the running pipeline/build/test running label Nov 27, 2024
@FedericaBrando
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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.

@FedericaBrando
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The new vep.tsv.gz is located here: /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
-

@koszulordie koszulordie linked a pull request Jan 2, 2025 that will close this issue
@FedericaBrando FedericaBrando linked a pull request Jan 7, 2025 that will close this issue
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