imgag/ClinCNV

Is it possible to add mitochondrial DNA cytoband information?

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Krutik6 commented

Dear developers,

I am using your amazing tool for germline WES analysis. It works pretty well I think.
I was wondering if there was a way to use clinCNV for mitochondrial analysis. At the moment, I remove any chrM samples I have because the cytobandsHG38.txt file does not contain any chrM information. Is there a way to add chrM information to the cytobandsHG38.txt file?

Many Thanks,
Krutik

GermanDemidov commented

Dear Krutik,

thanks a lot for your positive feedback! I think MT analysis is not that easy since it is always looking for "mosaic" CNVs and germline ClinCNV verstion works, assuming that the default copy-number is 2 and the deviation from this number is stricktly integer (0,1,3, etc). Of course, males and chrX/Y are a special case and handled differently.

Theoretically I think it is possible to put

chrMT 1 1 p11.1 16569
chrMT 1 1 q11.1 16569

but I doubt ClinCNV is a good instrument to solve this. Normally MT is sequenced as a whole, so I'd use Manta and paired-end information to call CNVs disregarding ploidy in MT.

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Krutik6 commented

Hi German,

Thanks so much for the detailed explanation, it really helps. I will look into these other tools.

Cheers,
Krutik