about CpG number in modbam2bed output

[kaanokay]

Hi,

When I run modbam2bed for CpGs, does the output has all CpGs in the genome or only those CpGs that have valid coverage. Namely, can I find all CpGs in a sample from modbam2bed output?

Bw.

[cjw85]

The code will output positions where there is at least one spanning reads, not every possible reference CpG.

[kaanokay]

Thank you.