Hi all, question. I ran a big batch of WGS samples using sarek. Using NGScheckmate we found that a few samples were incorrectly matched. I want to rerun tumor/normal variant calling for the wrongly matched samples. I didnt want to rerun all the allignment steps, as it does not matter yet that they were wrongly matched. However, the output BAM stores the sampleID_fileID info which now changed to the correct_sampleID_fileID. Is tried to use the samtools reheader function but it now does not like my BAM file anymore. Any tips on best practices to resume from here? Thanks for the help

NGSCheckMate has proven invaluable to me so many times I don't think there is a nice way to deal with this inside the pipeline. What doesn't like your bam file after you reheader it?

And thanks again @Simon Pearce for the addition

What did you do to "reheader" the files? I think if you just swap the headers, there should be little chance to introduce mistakes. Then you can run the pipeline again from

--step variant_calling

(I would do that from a new directory and with a new output location, to avoid overwriting any files).