Takes *selfSM reports generated by VerifyBamID during alignment, and returns a vector of freemix scores. The freemix score is a sequence only estimate of sample contamination that ranges from 0 to 1.
Note: Targeted panels are often too small for this step to work properly.
process.sample.contamination.checks(project.directory)Path to project directory. Each sample should have its own subdirectory
freemix.scores Data frame giving sample contamination (column freemix) score per sample.