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bbglab / intogen-plus

a framework for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients.
https://www.intogen.org/search
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IntOGen Plus | Add filtering of MNVs to the parsed output of VEP #27

Open FedericaBrando opened 5 months ago

FedericaBrando commented 5 months ago

As of now the filtering of MNVS is done in a very dirty way, with a step in nextflow that outputs the following:

SYMBOL  sample_id       COHORT  pos     MNV
A1CF    P03-1426        CBIOP_WXS_PRAD_BROAD    50816101        False
AAAS    PR-2916 CBIOP_WXS_PRAD_BROAD    53308786        False
AADAC   P05-620 CBIOP_WXS_PRAD_BROAD    151814177       False
AADAC   P06-2325        CBIOP_WXS_PRAD_BROAD    151827662       False
AADACL3 P00-000450      CBIOP_WXS_PRAD_BROAD    12725269        False

This can be incorporated in the mutations.py, as another output.