There are two BED files for CpG sites from Watson and Crick strands, respectively, which are required by the script of bsalign2jag_index.pl.

E.g.
perl  bsalign2jag_index.pl hg19.W.CG.bed hg19.C.CG.bed demo.W.rmdup.bsalign demo.C.rmdup.bsalign >Jag_index.txt

