liftfilter - merge lifted entries to the same position

Synopsis

$ dnmtools liftfilter [OPTIONS] -o <output.meth> <input.meth>

Description

The fastlift program may report multiple mm9 sites mapped to a same position in hg19. In this situation, we may either collapse read counts at those mm9 sites, or keep the data for only one mm9 site. We can use the lift-filter program to achieve these two options. Use

$ dnmtools liftfilter -o output-filtered.meth input.meth

to merge data from mm9 sites lifted to the same hg19 position. Use the option -u to keep the first record of duplicated sites.

Options

 -o, -output

Output processed methcount [required]

 -u, -unique

keep unique sites

 -v, -verbose

print more information to STDERR as the program runs.