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Pipeline to run BWA + GATK on a Illumina sample.
Ruby
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README.rdoc
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mutations_caller_pipeline_aws.gemspec

README.rdoc

Mutations Caller Pipeline (AWS)

This pipeline was created to automate several steps in the first part of a sequence analysis. The steps are basically the mapping of reads in fastq files, the preparing of the resulting raw bam files and the variation calling in the end. The pipeline will make it easy to get from fastq to vcf file, without running all the single steps in between. It is designed for to run on a cluster like AWS.

Unfortunately this is only a first edition, which is fully functional but poorly tested and the pipeline can not restart itself if there happens to be any errors.

License

This source code is licensed under the GNU General Public License (GPL-2.0) (opensource.org/licenses/gpl-2.0.php).

Install

The easiest is probably to install it via RubyGems, where you can just type

% gem install mutataions_caller_pipeline_aws

An alternative way …

… would be to clone the master branch in a desired directory:

% git clone git://github.com/khayer/mutations_caller_pipeline_aws.git

To install the gem you will now need to type

% cd mutations_caller_pipeline_aws
% rake

Config File

This file should be in the ruby .yml format. In this file you will need to include the directories to bwa, GATK2 and Picard.

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