methylcx extracts cytosine methylation information in all contexts (CpG, CHG, CHH) throughout the entire genome. The program receives an alignment file in BAM, CRAM and SAM formats as input. This file must have additional methylation information (tags) and read orientation (XR) and genome orientation (XG), generated by the Bismark program. The program generates a file containing information on all cytosines along the genome with tape information. This file uses the HDF5 format. The program also generates files compatible with Bismark, such as bedGraph and cov and cytosine-report.