process.sample.contamination.checks {varitas}

Process sample contamination checks

Description

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.

Usage

process.sample.contamination.checks(project.directory)

Arguments

project.directory

Path to project directory. Each sample should have its own subdirectory

Value

freemix.scores Data frame giving sample contamination (column freemix) score per sample.

References

https://genome.sph.umich.edu/wiki/VerifyBamID