Detecting contamination using schmutzi

This is intended to provide a little hands on experience with schmutzi by G. Renaud et al and is solely designed to provide some more detailed step-by-step information on how to determine contamination using the tool. If you find bugs in this, I’m happy to fix them; if you find bugs in the tool itself, please use the projects GitHub repository to open issues for them here . This is _not_ my tool, but I happen to be one of the more frequent users of the method, thus this was basically writing up things I found out myself or with help from the developer(s).

Contents:

• Detection of contamination on mitochondrial data
  • Sample preparation
  • Damage based contDeam
  • Mitochondrial based schmutzi
  • Output interpretation
  • Consensus Calling for Downstream analysis