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Published 20 hours ago • verified publisher icon nf-core

MSIsensor for tumor-only

Open jfnavarro opened this issue 3 years ago • 2 comments

It would be nice to add a process to compute MSIs for tumor-only samples:

https://github.com/niu-lab/msisensor2

I could take care of this.

jfnavarro avatar Jan 20 '21 14:01 jfnavarro

Hi! i looked into this a bit, looks like you need to create a baseline form public data beforehand. To ensure this is all in the right container and reproducible etc, I think we would need a bit of a change of the input,...maybe allowing two inputs...? not sure..i would say we can maybe push this to 3.1

FriederikeHanssen avatar Feb 11 '22 17:02 FriederikeHanssen

Hi! I started working on integrating the msisensor2 module into sarek, but unfortunantely it only takes bam as input. So I opened an issue - maybe they can integrate cram input into msisensor2 in the future.

SusiJo avatar Oct 17 '22 08:10 SusiJo