mitochondrial DNA in vcf for haplogrep2

Question

[biosol]

Hi everyone,

I'm trying to analyse mitochondrial data from human samples, which I have stored in a vcffile. I've tried running Haplogrep2 (both cmd and online) but my results do not make sense. Reading other posts, I've realised that I should first align my data to the rCRSsequence, so I was wondering which tool to use... can please anyone suggest one? Or does Haplogrep2 directly align vcfs to the reference sequence?

I have another doubt as well: my vcfhas 0/0 and 1/1in every position, but... isn't mitochondrial DNA a single molecule?? Shouldn't I only have one allele??

Thanks in advance!

[Arup Ghosh]

Haplogrep only supports rCRS/RSRS in the chromosome field in input files(VCF). The tool that has been used to call the variants uses ploidy 2 by default thats why you get 0/0 and 1/1.