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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 | Update cbase container version from v1.1 to v1.2 #29

Open migrau opened 4 months ago

migrau commented 4 months ago

Description

As we did recently https://github.com/bbglab/intogen-plus/pull/15 , update cbase to v1.2.

Changes relative to the legacy version CBaSE v1.1:

Export of many new estimates (see above):
Magnitude of selection: dN/dS, dM/dS and dK/dS.
Mutation target sizes for missense, nonsense and synonymous mutations.
Expected number of missense and nonsense mutations under neutrality.
Distribution of missense and nonsense mutations per gene (per tumour) under neutrality.
Expected value of lambda_s|s_obs.
Possibility to use vcf files as input, supporting both the hg19 and hg38 genome build.
Accounting for transcription strand bias.
Removal of pseudocounts in the pentanucleotide matrix.

FYI @FedericaBrando I'm volunteer for it, or if you prefer to do it, let me know :)