At the request of Stephan Beck's group, we ran Control-FREEC (v11.6b) on the EpiRRs listed in ihec_cancer_54.csv using the WGBS gemBS bam files. 
Control-FREEC was also run on a subset of these EpiRRs for which WGS data was available.

The following paramters were specified in the config files:
[general]
maxThreads = 6
ploidy = 2,3,4
breakPointThreshold = 0.8
window = 50000
[sample]
inputFormat = BAM
mateOrientation = FR

Results were generated by Jonathan Steif