I am working on WGBS for strawberry (Fragaria vesca) genome. I want to annotate CpG,CHG and CHH islands in the genome. The recent version of the genome has a transcript gff3 file and a genes gff3 file. I am using the methylkit to annotate differentially methylated bases /regions and methylkit requires a bed file for annotation.I have converted the transcript gff3 file to bed.However, I am not able to convert the genes.gff3 file to a bed because the file lacks the first line.When i cheched the file using gff3 validator, it shows that the file lacks the first line denoted as " ##gff-version 3". My questions are:

1. How can I insert the line" ##gff-version 3" in the gff3 file.
2. Can anyone help calrify if any of the above mentioned gff3 files contain information about CpG, CHH and CHG features? if not.
3. Where can I get a gff3 file or bed file that can be used for annotating CpG,CHG and CHH.

I appreciate your help.