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Python implementation of Java SNP calling pipeline (https://github.com/DSGlab/SNPCallingPipeline/)

Project description

ABOUT
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Python implementation of Java SNP calling pipeline (https://github.com/DSGlab/SNPCallingPipeline).
Usage is descriped below. For consistency the configuration file is exactly as described in the Java code.
Descriptions of the various options in the Java code is given at https://github.com/DSGlab/SNPCallingPipeline.
An example configuration file is included in this directory.
USAGE
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usage: pySNPCallingPipeline.py [-h] -c CONF_FILE [--aln_only] [--no_aln]
[--local] [--submit] [--subset SUBSET]
[--def_run]

Run pySNPCallingPipeline

optional arguments:
-h, --help show this help message and exit
-c CONF_FILE, --conf CONF_FILE
A configuration file is required to run
pySNPCallingPipeline.
--aln_only Alignment only, default is FALSE.
--no_aln Run all analysis using pre-run alignments, default is
FALSE.
--local Is this a LOCAL run or should SLURM files be created?
Default is True.
--submit If running a supercomputing cluster, should only slurm
files be created or should the jobs be submitted as
well.
--subset SUBSET Provide a comma seperated list of a subset of
"alignment, getHQSNPs, intraClonalSNPs, checkSNPs,
filterSNPs"
--def_run Default: run entire calculation locally.



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