See https://github.com/uwescience/sqlshare/wiki/Workflow:-Analysis-of-BSMAP-data for background.
GFF format was created from methratio file that only has info for CpG and 10x coverage
SQLSHare Code
SELECT
chr as seqname,
'methratio' as source,
'CpG' as feature,
pos as start,
pos + 1 as [end],
ratio as score,
strand,
'.' as frame,
'.' as attribute
FROM [sr320@washington.edu].
[BiGO_betty_plain_methratio_v1.txt] betty
where
context like '__CG_' --_=single character wildcard
and
CT_Count > 9
Also will create new gff with 5x coverage in SQLShare
!head /Volumes/web/cnidarian/BiGO_Methylation5x_oysterv9.gff