Mitochondrial variant calling pipeline missing a step

[Rohit-Satyam]

Hi @grbot

I see that the mitochondrial variant calling pipeline excluded "Align the unmapped BAM file with the reference aligned BAM and shifted reference aligned BAM" step described in mt-variant calling gatk pipeline. Any particular reason for that. I am asking this because I don't understand this step either and was wondering if this is really necessary ?

I can see shifted reference fasta available here

[grbot]

@Rohit-Satyam the time that the workflow was created that step was not part of the GATK best practice. We would need to update the workflow to include the additional steps. At the time there is not a high priority for this. Are you planning to run this workflow?