"best contig too short to make mutation" / "No good alignment between mutated contig and original, aborting mutation!" Errors

[FelipeAze]

Hello Adam!

I'm trying to use BAMSurgeon to create in-silico deletions on mitochondrial DNA, using the SV module. I have a set of samples with a median coverage around 200x. But, for most of them, when I try to insert any mutations at least one of the following messages appear:

WARNING 2023-08-02 18:10:39,873 chrM_167_167_BIGDEL best contig too short to make mutation!
WARNING 2023-08-02 18:17:40,804 chrM_83_83_BIGDEL No good alignment between mutated contig and original, aborting mutation!

Do you know what might be causing these issues?

Thanks,

Felipe