Multireg
Format
cg multireg ?options? compar_file ?file? ...
Summary
Compare multiple regions files
Description
This command is used to create multiregion compar_files. These are
tab separated files indicating which regions are present in multiple
samples. The first columns indicate the position of the region using
the chromosome,begin,end columns. These are followed by columns
containing 1 if the region is present in samplename and 0 if not.
Arguments
- compar_file
- file containing regions, and columns indicating the presence
of the region
- file
- region files to be added the compar_file. The name of the
column is name of the file added without extension
Options
- -m maxopenfiles (-maxopenfiles)
- The number of files that a program can keep open at the same
time is limited. pmulticompar will distribute the subtasks thus,
that the number of files open at the same time stays below this
number. With this option, the maximum number of open files can be
set manually (if the program e.g. does not deduce the proper limit,
or you want to affect the distribution).
- -limitreg regionfile
- limit multireg to regions in regionfile
This command can be distributed on a cluster or using multiple
threads with job options (more info
with cg help joboptions)
Category
Regions