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)
Process_multicompar
Format
cg process_multicompar ?options? projectdir ?dbdir?
Summary
process a sequencing project directory. This expects a genomecomb
directory with samples already processed and makes annotated
multicompar data
Description
This command runs the multicomparison step of cg process_project. As input, the
command expects a basic genomecomb project directory with sequencing
data (projectdir) for which the samples have already been processed.
Some of the steps/commands it uses can be used separately as well:
Arguments
- projectdir
- project directory with illumina data for different samples,
each sample in a sub directory. The proc will search for fastq
files in dir/samplename/fastq/
- dbdir
- directory containing reference data (genome sequence,
annotation, ...). dbdir can also be given in a projectinfo.tsv file
in the project directory. process_illumina called with the dbdir
parameter will create the projectinfo.tsv file.
Options
- -split 1/0
- split multiple alternative genotypes over different line
- -dbdir dbdir
- dbdir can also be given as an option (instead of
second parameter)
- -dbfile file
- Use file for extra (files in dbdir are already
used) annotation
- -targetvarsfile file
- Use this option to easily check certain target
positions/variants in the multicompar. The variants in file
will allways be added in the final multicompar file, even if none
of the samples is variant (or even sequenced) in it.
- -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).
- -varfiles files
- With this option you can limit the varfiles to be added to
the given one. They should be given as a list of files in this
option, so if using wildcards, enclose in quotes.
This command can be distributed on a cluster or using multiple
with job options (more info with cg
help joboptions)
Category
Process
