I have a question about the Mitochondrial short variant discovery documentation. In the "Align the unmapped BAM file with the reference aligned BAM and shifted reference aligned BAM" step, I don't understand which is the shifted reference BAM. Do we have to create a new reference and map against it? If so, how do we create the shifted reference?
The input required is only a BAM aligned against the full genome, isn't it?
Maybe it's something obvious, but I can't see it, I'm sorry.
Please sign in to leave a comment.