CNV tools for mitochondrial chromosome using whole-genome sequencing

Question

[hellbio]

Could someone suggest any tools that work well for mitochondrial cnv detection using whole-genome sequencing data? Thanks!!

Answer 1

[QVINTVS_FABIVS_MAXIMVS]

If you want to find mitochondrial insertions INTO the human genome DINUMT

For SV in the mitochondria genome I know Manta and possibly lumpy (I don't have raw lumpy output at hand right now) will call SVs within the mitochondria

You might want to look into INDEL callers too since you do not expect to see a SV >5kb in the mitochondria. Haplotype Caller, FreeBayes, Platypus, and Scalpel are programs my lab works with (not me personally)

Answer 2

[liufengxia9999]

hi, have you found the right tool for mitochondrian CNV ?