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Call mitochondrial chromosome (mitochondrial sequence) from whole genome sequence


I wonder if there is any commands purposely for mitochondrial sequence calling. I do have a whole genome sequence (in .bam), but now I want to call only the mitochondrial part of the sequence. Is it possible? Is there any command respective to it?

Also, is it possible for me to call the single nucleotide polymorphisms (SNPs) that located in mitochondrial part? Do I have to use commands for that also?

I am glad to hear from you guys. Anyway, thank you in advance!



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