Friederike Hanssen

Mainly user requests of getting metrics after both steps. Ups estimatelibrary complexity is only done after MD, little c&p error

I was not involved in the original decision to use qualimap. @maxulysse do you remember the reasoning? I looked a little into replacing it at some point (since we use...

Hey @abhi18av ! What is the status here?

ok, then let's leave this issue open :) Thank you, I tried to clean up a bit before tomorrow

Should we move this issue to modules? Not exactly a sarek related one

as mentioned in the other PR I like `aligned_input` or `input_aligned` for bam/cram/sam and then `aligned_index` for bai/crai/sai

This also is the case for `Markduplicates` with output `cram` and `cram.bai`

Yes we have talked about it quite a bit. However, before we do that we need to find a solution for snpeff annotated files and the merged ones. vcf2maf only...

Tagging @adamrtalbot @c-mertes @ggabernet @asp8200 @jemten as we all are trying to do similar things and could join forces 🚀

what tool are you all using for the evaluation of the vcfs? hap.py/som.py?