mutect2-realigned .bam output

[seedgeorge]

Description of feature

I think that Sarek should have a flag for spitting out a mutect2-created .bam file delineating the variants it is considering. This is not a default option for Mutect2 but one that I think can be of great use to users, because Mutect2 performs realignment of the reads, meaning the calls it makes may not be perfectly obvious from the original .bam file. Being able to compare the two is quite reasonable I think, although since not everyone will be interested in this level of scrutiny, I think it should be an optional parameter.

It can currently be partly solved with a custom process config to modify mutect2 at the command line level, which from my testing will succeed in instructing the individual process to output such a .bam. It is technically possible to extract these .bams - but the user will have to merge them (because they are parallelised) and then sort and index. I think that Sarek should do this as an option, and that this is within the scope of the pipeline.