I have downloaded a WGBS file from ENCODE in bedMethyl format (https://www.encodeproject.org/experiments/ENCSR890UQO/). The content of this file is the methylation state per CpG, e.g.:
track name="SL1615 MspIRRBS" description="GM12878-16_Ximat" visibility=2 itemRgb="On" chr1 100003153 100003154 ...[omited] 2 0 chr1 1000170 1000171 ...[omited] 22 0
What I want to have is a bed file containing larger regions, somewhat like peaks called from the file above. Is there a tool available that can perform this task?
(My ultimate goal is to use the peak information to state whether an certain region in the genome (e.g. a promoter) can be called "methylated".)