search

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
395 stars 402 forks source link

Allow genotyping germline sites with Mutect 2 #1049

Open lbeltrame opened 1 year ago

lbeltrame commented 1 year ago

Description of feature

Some software, like PureCN, expects to have germline sites called along with somatic sites when using MuTect 2. However, currently there's no way to set --genotype-germline-sites true and --genotype-pon-sites true to the caller arguments, or at least not that I've found with a search in the workflows.

This should be optional, and default to off.

Reference: https://bioconductor.org/packages/3.16/bioc/vignettes/PureCN/inst/doc/Quick.html#3_Create_VCF_files

FriederikeHanssen commented 1 year ago

I am not exactly sure, what you want, but if it is running mutect2 with some custom parameters, you can do so easily with a custom config: https://nf-co.re/docs/usage/configuration#understanding-and-modifying-tool-arguments

lbeltrame commented 1 year ago

Thanks, for now that will do. However, in the context of #95 and in particular for PureCN support (where I and @aldosr have been adding the required modules to nf-core to this purpose) this may need to be bolted on to sarek in the future.