I am using BISCUIT for WGBS data. After the full process BISCUIT provides bedgraph file with CpG and corresponding methylation value. However, I am wondering how BISCUIT figure out which read should be considered in a bam file for methylation value calculation? For example, in the biscuit tview image there are 14 non duplicated reads (all has mapq=60) for the highlighted CpG. However, the generated bedgraph file is saying that the depth is 10 (5th column).
chr1 1222700 1222702 0.901 10 C:0.670:3,G:1.000:7
I am wondering what is the technique to calculate methylation value from the raw bam file for a certain CpG?