Tools to detect CNV for NGS-mtDNA

Question

[NB]

Hello,

Wondering if there are tools to detect CNV (duplications and deletions) for mitochondrial NGS analysis (clinical setting) ? Not sure if I can use ExomeDepth for the same ?

Thank you

[WouterDeCoster]

I assume you sequenced the mitochondrial genome entirely, and not as in WES just parts of it?

Given that chrMT is so gene dense, I'd think that if you perform target enrichment for the coding sequences you still sequence everything...

I would not use a depth based CNV caller, but rather something like Lumpy.

[NB]

yes, its only the mtDNA that has been sequenced entirely . Does Lumpy include the breakpoints info for each CNV detected ?

[WouterDeCoster]

I'm not sure, but the paper sounds promising. I assume you have pretty high coverage of chrMT. An additional problem is the possibility of heteroplasmy - and not just a simple diploid situation. That might suggest you should look at SV callers for cancer - but that's not my cup of tea.

[NB]

okay, i'll try out a couple of CNV callers.