GenomeComb

Regextract

Format

cg regextract ?options? cutoff file1 file2 ...

Summary

Find regions above or below a given cutoff.

Description

Write a regionsfile to stdout that contains all regions in the given files that are above or below a given cutoff. Each file contains data for one chromosome. Chromosome name is taken from the filename by splitting on "-", and taking the second element.

Arguments

cutoff
cutoff
file1
file containing position and value columns, or bcol file.
...
other files

Options

-qfields
list (separated by spaces) of possible fieldnames to use as values for the cutoff; The first in the list that is in the header will be used (default = "coverage uniqueSequenceCoverage"). This option is not used for bcol files, as they contain data for only one "column".
-posfields
list (separated by spaces) of possible fieldnames to use as position; The first in the list that is in the header will be used (default = "offset pos position begin start"). This option is not used for bcol files.
-above
1 if regions should contain values > given cutoff. defaults to 0, meaning values should be < the cutoff.
-shift
change the position by the given amount, e.g. -1 to change from 1-based to 0-based coordinates

Category

Regions