If I use an externally-made BAM, how can I tell sarek not to look for sample names that are

PatientID_SampleID

in the BAM header when using it in the variant calling step as normal? Otherwise MuTect2 puts

PatientID_SampleID

as normal sample in the CLI, and it breaks (because the

SM

tag in the BAM is different)

we have exactly that issue in the tests

That will work if you have one normal, right?

Thanks Rike, that was faster

Oh, completely forgot about

meta

! That will work