question about reference fasta

[snackens]

Hi, thank you for this convenient tool.

I'd like to call variants using human mtDNA. In the reference_genomes.tab, we need to specify ref_genome_mt and ref_genome_n.

I'd like to use hg19 as a reference. I downloaded genome data of hg19, but this genome data include chrM(and chrMT).
Should I remove mtDNA sequence from hg19 genome date when I use hg19 as ref_genome_n?
then Should I speficy rCRS fasta data for ref_genome_mt?

best regards,