7 add small variant list module

[marrip]

Hey guys,

here is my first draft for the module that should update the small variant vcf list. Our code at HUS might be different from your nodes so we need to discuss if the changes we made would work forall other nodes (I included at least one representative from each node now). I have some very old code from OUS which does not check for control samples and does not remap certain tumor types so please let me know if that is something we don't want a.k.a. only HUS wants.

I guess you might have concerns about where the files are put. For now, let's not focus too much on that. We can change these paths later and create specific profiles for each node.

I also thought that this bash script is a bit clumsy and maybe we want something in python instead doing all of this. I would volunteer to put something together in case we agree to go that route. Also, for me it would make sense to not update but rather recreate the file each time we run this process and just glob all runs' small variant vcf files, remove control samples and remap sample types (if we agree on that), exclude vcfs/samples/patients we don't want (have a blacklist of those somewhere), and finally sort and uniq the list.

Please reach out in case you have questions either on Teams or here. We can also do a meeting if that is easier for you.

Your feedback is highly appreciated 🙂