Friederike Hanssen

Oh on problem I see now, is that I updated a bunch of gatk modules over Christmas , that use intervals, because we usually have multiple intervals per patient. Sorry...

applybqsrsoark has a mismatched checksum, why can that not be fixed?

https://github.com/nf-core/modules/pull/1965#discussion_r999479089 all the version.yml are removed, from here I gather this may not be intentional. might be worth to wait until this is cleared up

😵‍💫 sorry, weird it didn't upload the file. it doesn't want to upload the html file. give me a sec

[1234N.summary.html.txt](https://github.com/ewels/MultiQC/files/8661665/1234N.summary.html.txt)

Ok this is starting to take shape. A couple of things that I could use help with: 1. generating the yml files for VEP, Strelka, & Freebayes. 2. Which parameters...

> Hello @FriederikeHanssen @apeltzer, > > I am the co-developper of pyTMB, I'm working with Nicolas Servant. > > Thanks a lot for your help for bioconda ! I was...

some docs on computing VAF for germline samples would be great. I guess we should divide the second value from the AD list by DP?

Bumping this question: can I use batch on the normal, unpaired, WGS samples if I create a flat reference?

Read the docs: https://github.com/BoevaLab/FREEC/blob/271bef4777119e69ae6eaf1e68051e12fae5e529/scripts/makeGraph2.0.R#L5 I think we don't need to supply the ploidy