GIML produces segmentations of methylation data generated by whole genome bisulfite sequencing
(WGBS).
The coarsness of the segmentation is controlled by a parameter called
giml <input-file> <lambdas>
input file is a file in tab-separated format:
chromosome position non-converted-reads converted-reads if the file name is '-' giml will read from the standard input.
One can specifiy more tha one lambda by using ":" as a separator. The different lambdas will be tried in sequence.
tab-separated format:
chromosome segment-start segment-end lambda index-start index-end methylation-mle
where index-start and index-end are indexes for the segment into a zero-based array which stores the positions of the chromosome (useful for plotting and counting the CpGs contained in a given segment).
the giml repository contains scripts to perform basic descriptive statistics on giml output, and to help plotting the segments.