Comparative analysis of experimental and control data from BS seq run

Question

[kspata]

Hi All,

I have one control sample and 3 experimental samples sequenced on HiSeq using Bisulfite sequencing protocol. I aligned the reads to the hg38 genome and performed methylation calls using standard Whole Genome Bisulfite bismark pipeline.

I wish to perform comparative analysis between experimental and control set. I want to know which CpG sites were methylated or not between these groups and annotate those sites.

I have the BAM files and methylation call files from this experiment. What tool can I use to perform above analysis.

Thanks in advance!!