Calling mitochondria DNA variants setting

[freedomq8]

Hi there,

I am trying to find out what are the best settings/options/data to use with strelka to call variants of mtDNA across a number of exome samples (mapped to b37 assembly).

I used the germline workflow with and without "--callContinuousVf" MT flag which made a big impact on the final results size. I also saw the flag "--ploidy", I think the ploidy flag with strelka is different than GATK flag which were used to choose haploid and diploid sample, I thought this would be useful to include with "--callContinuousVf" and without and see the impact on the result, however, I tried to add "1" after the flag but its not recognized.

So my question is what is the best combination of settings to use for calling mtDNA variants: shall I use germline workflow or somatic ? is there a specific data I should include a dataset while calling the variants to optimize the results? and finally what is the best flags to use for mtDNA ?

Thanks