sarek
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MSIsensor for tumor-only
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.
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
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.