I am currently working on GATK's new best practice for mitochondrial variant calling. My data is WES. I read about the forum and wdl of GATK best practice. While I am confusing about the shifted chrM fasta, do I need to generate it by myself? For I could not just download from their web because the path is wrong when I used the one in json file.
Also their pipeline is based on hg38, and I use hg19. I think this doesn't matter because we just focus on chrM fasta, right? And should I use rCRS fasta as ref?