I am having difficulty in making bammds accept my aligned-sorted-deduplicated bam file.
I suspect that my version of the reference genome and the one your tool uses do not quite match; in other words, it is a similar situation to what was reported three years ago in this post
Since the link doesn't work anymore to get the reference genome from to the ftp site that was made available back then; would it be possible for you to send me instructions as to how to get a copy of it now?
Thanks in advance for the attention to this matter.