Which is the correct file to be taken from Bismark to methylKit?

The primary option would be to read in the SAM/BAM files and perform methylation calling in methylKit. However, it can also be done through bismark_methylation_extractor which produces context (CpG/CHG/CHH) dependent methylation call files containing the following columns:

<seq-ID> <methylation state*> <chromosome> <start position (= end position)> <methylation call>

This is not the expected input methylation call file as required by methylKit. As per the tutorial, a typical methylation call file should look like:

chrBase   chr    base strand coverage freqC  freqT

Other options include creating bedGraph coverage file or cytosine report.

So which of the possible output files from Bismark be taken into methylKit?