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Python implementation of Java SNP calling pipeline (

Project description

Python implementation of Java SNP calling pipeline (
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
An example configuration file is included in this directory.
usage: [-h] -c CONF_FILE [--aln_only] [--no_aln]
[--local] [--submit] [--subset SUBSET]

Run pySNPCallingPipeline

optional arguments:
-h, --help show this help message and exit
A configuration file is required to run
--aln_only Alignment only, default is FALSE.
--no_aln Run all analysis using pre-run alignments, default is
--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
--subset SUBSET Provide a comma seperated list of a subset of
"alignment, getHQSNPs, intraClonalSNPs, checkSNPs,
--def_run Default: run entire calculation locally.

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