Allele count of 2 for homoplasmic MT variants in VCF

Question

[Arton]

I have noticed that homoplasmic variants in VCF files generated by GATK HC have allele count of 2. I am wondering if this is a common practice in generating VCF files for mitochondrial variants?

[Ram]

Please stop using bioinformatics as a tag unless your post is about the field of bioinformatics itself.

Answer 1

[LChart]

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

[Arton]

Thank you for the helpful answer!

[GenoMax]

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