Allele count of 2 for homoplasmic MT variants in VCF
1 answer
The GATK (and afaik every caller that I know) treats every contig of the reference as having the same ploidy (so all haploid, all diploid, etc). You will also see diploid calls on X and Y chromosomes unless you call them separately. The mitochondria is simply another contig and is treated the same way.
The best practices (according to GATK) for processing the MT is here: https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels
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