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  1. Reference files: Human genome 
    1. Download the reference files using this link https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0;tab=objects?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false
  2.  Nextflow (https://www.nextflow.io/)
    1. Need to install nextflow in your work directory by using the command: curl -s https://get.nextflow.io | bash
  3. Singularity
    1. Need to load singularity module if using CAMH Specialized Computing Cluster: e.g., module load tools/Singularity/3.8.5
  4. Mutserve (https://github.com/seppinho/mutserve) 
    1. Need to install mutserve in your work directory by using the command: curl -sL mutserve.vercel.app | bash
  5. Our pipeline was adapted from https://github.com/gatk-workflows/gatk4-mitochondria-pipeline.
  6. PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/)
    1. PLINK 1.9 (https://www.cog-genomics.org/plink/)
    2. Need to load plink module if using CAMH Specialized Computing Cluster: e.g., module load bio/PLINK/1.9b_6.15-x86_64
  7. R (http://cran.r-project.org/)
    1. Need to load R module if using CAMH Specialized Computing Cluster: e.g., module load lang/R/4.0.3-Python-3.8.5-Anaconda3-2020.11
  8. Unix-based command terminal
  9. A text editor

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