Convert hg19 to rCRS positions for chrM

[Vasilisa]

Hi all,

I have a list of SNPs (vcf file) for chrM originally obtained using hg19 as a reference genome. I would like to convert the positions so that they correspond to rCRS (revised Cambridge Reference Sequence).
Is there a simple way to do this?

Thanks!

[pguilha]

Any answers?

About three years on, and I'm having the same issue.
I'd like to avoid having to realign all my fastqs to a different reference and I already have bams with only mitochondrial reads in them.
I'm currently trying to get the the old liftover script provided by GATK to work but if anyone knows of a better way to do this it would be much appreciated!
cheers