What is the right place of the most recent mitochondrial analysis pipeline? Is it in this workspace https://app.terra.bio/#workspaces/gatk-workflows/Mitochondria-SNPs-Indels-hg38%20copy in Terra? If so, is this pipeline enough to run the full analysis as performed in the paper https://www.biorxiv.org/content/10.1101/2021.07.23.453510v1.full.
At first I came across this pipeline https://github.com/gatk-workflows/gatk4-mitochondria-pipeline from gatk-workflows on Github. I used it locally.
In the paper, it is stated that the following is performed to do the whole analysis including filtering, annotation... "The Mutect2 pipeline is available through GATK at https://github.com/broadinstitute/gatk/blob/master/scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl (the data available in gnomAD v3.1 was generated using https://portal.firecloud.org/?return=terra#methods/mitochondria/MitochondriaPipeline/25), and the Hail scripts used for combining the VCFs, filtering samples and variants, adding annotations, and performing analyses can be found at https://github.com/broadinstitute/gnomad-mitochondria."
Could you please guide me in specifying the right pipeline workflow? If the workflow in Terra is performed then the outputs can be used to run the Hail scripts?