What are the necessary input files of the Genome Integrity pipeline?

1. If running the Genome Integrity pipeline alone, the necessary input files are:
2. 1. 1. Reference genome
      2. DNA panel files NOTE: these must be formatted specifically for this pipeline
      3. Spike-In CNV file
      4. Whitelist/Blacklist Variants File
      5. Spike-in Variants File
      6. DNA Fastqs and protein Fastqs for DNA + Protein runs
      7. Protein panel file is required for DNA + Protein runs

These are described in more detail here.

2. If running the GE pipeline first, those input files are:
   1. Reference genome
   2. GE DNA panel and protein panel for DNA + Protein runs (NOTE: one additional file is required for GE + GI runs, input files are detailed here.)
   3. Spike-in CNV file
   4. Spike-in Variants File
   5. DNA Fastqs and protein Fastqs for DNA + Protein runs

These are described in more detail here.