GATK has a best practices Workflow for SNV and Indel discovery in mtDNA: https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-

The pipeline for mitochondrial variant discovery, using Mutect2, uses a high sensitivity to low AF and separate alignments using opposite genome breakpoints to allow for the tracing of lineages of rare mitochondrial variants.

It is described by its general steps but not with specific command code. This workflow seems more complex than a normal autosomal variant calling pipeline, but it also explains the complexity and problems of this task.