Mutect2 for mitochondria variant discovery

Question

[ernestine.kubi]

I am following the pipeline for mitochondria variant discovery using mutect2. I am currently trying to Align the unmapped BAM file with the reference aligned BAM and shifted reference aligned BAM using the MergeBamAlignment command. I keep getting error. Can anyone help?

[GenoMax]

I keep getting error.

Without providing information about the actual error no one can help. Please edit the post and add this information.