melbournebioinformatics/exome_variant_calling_pipeline-bpipe

Name: exome_variant_calling_pipeline-bpipe

Owner: Melbourne Bioinformatics

Description: null

Created: 2014-05-09 01:17:15.0

Updated: 2017-05-09 08:08:17.0

Pushed: 2014-05-26 07:16:12.0

Homepage: null

Size: 182

Language: Groovy

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README

Exome Variant Calling pipeline - Bpipe

An exome variant calling pipeline written in Bpipe

Usage: bpipe run pipeline.groovy *.fastq.gz

Set up:

Edit the locations of installed software, reference data, target region etc. in pipeline_stages_config.groovy

Requirements:

Software:

• FASTQC 0.10.1
• BWA 0.7.5a
• Samtools 0.1.19
• Picard 1.96
• GATK 2.8-1

Reference data:

• GATK reference bundle

Note: Tested with the above versions, but may work with other versions.

Pipeline tool:

Bpipe code.google.com/p/bpipe/

Requires a variant of the bpipe script to handle module specification. If this is not used, then the required modules must be loaded in the relevant .bashrc script.

bpipe variant: slugger70-bpipe

Pipeline overview:

• Check reads (FastQC)
• Align reads to reference genome (BWA mem)
• Improve alignment (Picard, GATK)
• Call variants (GATK)