process.sample.contamination.checks: Process sample contamination checks

In varitas: Variant Calling in Targeted Analysis Sequencing Data

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

varitas documentation built on Nov. 14, 2020, 1:07 a.m.