BoostDM Connection

IntOGen pipeline integrates the generation of files needed to run by BoostDM [1] in order to keep a unified data and software environment and limit preprocessing of input for BoostDM as much as possible. The integrations consists in two new steps in the pipeline:

DriverSaturation

It computes all the possible mutations for a given gene mapping to the MANE transcript. It uses VEP v111. Specifically, it considers both the exons of the transcript and intronic sites within 25 bps distance from the intron-exon junctions.

Filter MNVs

Individual SNVs in adjacent positions reported in the same sample are discarded as potential multiple nucleotide variants (MNVs) that are wrongly called as separate SNVs.

Parse Profile

Profile output by ComputeProfile step is parsed in a 96-channel for every trinucleotide context, to ensure consistency and compatibility with BoostDM run.

[1]

Ferran Muiños, et al. In silico saturation mutagenesis of cancer genes; Nature 2021. (https://doi.org/10.1038/s41586-021-03771-1)