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

nf-core

At some point in the future I might need to analyze data with low-frequency variants. I see that Sarek implements LoFreq for this, but it's only available in tumor-only mode. Is there any reason not to pass (only) non-tumor samples as tumor in the samplesheet to make it work?

None in my opinion, I guess it was added that way because of usage

Mixed germline samples is a niche use case, but so is my entire project

Does Sarek implement `lofreq indelqual` ? According to <https://csb5.github.io/lofreq/commands/|the docs> it's necessary for samples without BQSR (which is the case for me) if indel calling is desired (which is also the case)

I don't see it looking into the code but I'm asking before opening an issue

<@U065DAZ0PL5> implemented LoFreq, maybe she can calirfy a bit more

No I did not implement lofreq :see_no_evil: It was added by some people but there is also something a bit off with the implementation (I think there is an issue for that somewhere) <https://github.com/nf-core/sarek/issues/1963> - as in lofreq is implemented as tumor-only but I believe it should be a somatic caller