GATK's new best practice for mitochondrial variant calling

Question

[lovelysunzt]

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?

[guofengwang123]

I come across the same question that confused me . Have you got the answer?

Answer 1

[sriram_pharm]

You can generate it using the ShiftFasta tool in GATK https://gatk.broadinstitute.org/hc/en-us/articles/4413079325595-ShiftFasta-BETA. For Human references, it is readily available on their cloud workflows but not for other organisms. In case it is for mouse or Drosophila, the tool shifts the reference to a point other than 1-16Kb which is say 8-16-1Kb relatively.