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mutect2 error with tumor-normal pairs starting from BAM files #1468
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I had a similar issue on 3.4.1, where it gave me an error about not having a |
Has this been resolved? I have an almost identical issue, also starting with variant calling from aligned bam files, and Mutect2 is also complaining that a sample isn't in the bam header. My samplesheet contains patient,sex,status,sample,bam,bai |
Hi, so I could resolve this error as following:
I overwrote this in the process scope of a separate config file provided with
So you either change this config file to fit your BAM sample names or another solution would be to rename the BAM samplenames, e.g. with |
Thank you so much! |
Is this also a problem with Sarek v3.4.2? |
Yes, I'm running |
Description of the bug
Hi, I run into the following error with running mutect2 via sarek:
It seems that there is something wrong with the mutect2 command in this configuration.
It defines a normal sample which cannot be found by mutect2 (from the
.command.sh
):Freebayes and strelka run fine without an error message.
I have the following configuration:
Can you help me fixing this problem?
Command used and terminal output
samplesheet (example):
run command:
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