A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hi all, I'm interesting in performing variant calling using only RNA-seq data (without matched normal neither matched WES/WGS).
With this pipeline, germline mutations are identified. Has anyone ever tried to extend the workflow to also include somatic mutations? Thanks in advance

As far as I know, not yet, but it is a request that was already made: <https://github.com/nf-core/rnavar/issues/241>
I am wondering if <#C03MDE53ZCP> couldn't be use for that particular purpose.
I am unfortunately lacking time to work on this issue for now, but I would happily guide you if you want to work on it

I do think we would need a PON, and/or germline ressources.

And possibly enhance the samplesheet to handle status

Thanks for your prompt response.
From the  from the GATK resource bundle , a reference for PoN and germline variants could be exploited maybe.
I checked in <#C03MDE53ZCP> but unfortunately these is still no updates regarding this threads of extending to somatic mutations.
An implementation from scratch for me it is not possible at the moment unfortunately , but it could be really beneficial

I'll see if I can whip something out with some AIsistance