gemBS aligner file format

Question

[shrinka.genetics]

Hello Everybody

Recently I got few files of WGBS data, which is aligned using gemBS. I have a question

How (Non-converted base count + Converted base count) is not giving the value of Total base. Does it mean that those extra values are for non CpG

This is my gemBS aligned file (header added)

Chr     Start   End    Ref call Genotype call   Methylation estimate    Non-converted base count    Converted base count    Total bases supporting genotype call    Total bases
chr1    10668   10669   G   G   1   3   0   6   6
chr1    10671   10672   G   G   1   4   0   7   7
chr1    10674   10675   G   G   1   5   0   10  10
chr1    10680   10681   G   G   1   7   0   12  12

Anybody, please comment on this

Regards Shrinka

[GenoMax]

gemBS output files are described here. See if that helps.