Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)

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).

This command can be distributed on a cluster or using multiple threads with job options (more info with cg help joboptions)

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