IntOGen plus | Update to MANE transcript

[FedericaBrando]

TO DO (Federica): Run some cohorts as tests, updating the pipeline → Filter for MANE-Select → For the moment do NOT include the MANE- plus clinical

0. Update VEP to last version (v110?)
1. Filter by MANE-Select Start with some cohorts to detect possible errors
2. Think about how to include MANE-Plus Clinical

[FedericaBrando]

• [x] Rebuild dataset and container for ensembl v110
• [x] reimplementation pipeline

[FedericaBrando]

analysis of differences:

• testing data

[FedericaBrando]

• [ ] update smregions.mk to MANE

[FedericaBrando]

[FedericaBrando]

maybe has something to do with :

[FedericaBrando]

Everytime the container vep is run we have this warning:

found github issue on their web:

• https://github.com/Ensembl/ensembl-vep/issues/1468

this PR will fix the warning on next release (v111)

• https://github.com/Ensembl/ensembl-vep/pull/1461

[FedericaBrando]

Therefore the error (warning) is in the container. The problem is that, since we build the cache dir with a loop through chunks where we call the vep container multiple time, we have a smartwatch warning for each call.

[FedericaBrando]

Run with MANE transcript:

• [x] TCGA
• [x] HARTWIG

[FedericaBrando]

waiting for monica to analyze

[FedericaBrando]

Some genes are no found in the datasets, Monica and I found out it is because they are filtered out in the ParseVep step. Specifically, an expected mane gene that is supposed to be annotated as mane, it is not.

I open an issue on vep github to report the bug.

• https://github.com/Ensembl/ensembl-vep/issues/1539

To overcome the issue, we decided to use two conditional filtering:

if the transcript does not have MANE, then use the canonical.

[FedericaBrando]

Ensembl was updated to v111.

[FedericaBrando]

• [x] Update to v111.
• [x] Run test cohort
• [x] Merged in develop along with cbase fix
  • https://github.com/bbglab/intogen-plus/commit/8dad37becca83a4823cee853d532780019be83b7
  • https://github.com/bbglab/intogen-plus/pull/15
• [ ] Run everything in develop branch

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Something to keep in mind is that with the update of Ensembl v111 some gene name will change.

[FedericaBrando]

TODO

updat boostdm DriverSaturation to use MANE

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DriverSaturation uses canonical.regions.tsv