This folder contains scripts to produce the tranche plots included in
the manuscript.  The R script provided to draw the plots was extracted
from GATK 4.0.1.2's jar file, and received only cosmetic changes
(titles, legends, pdf/png output).

The snp.tranches files provided in the subfolders were extracted from the
output from VariantRecalibration. The repository also includes a snapshot
of the generated png/pdf, as a convenience.