ssadedin/exome_depth_pipeline

A Bpipe pipeline for easily running ExomeDepth

exome_depth_pipeline

A Bpipe pipeline for easily running ExomeDepth.

Overview

ExomeDepth is a fantastic tool for identifying CNVs in exome or targeted sequencing data.

This small pipeline just makes it a bit easier to run by implementing a set of defaults that should work for most situations. With this pipeline you just need to supply the following:

• a set of BAM files - one sample per BAM file
• a BED file of the target region of your exome or targeted sequencing data
• the human genome reference FASTA to which the BAM files were aligned

Install

1. To run the pipeline you need to install Bpipe:

http://bpipe.org

2. Once you have done that, you can check out this pipeline anywhere:

git clone [email protected]:ssadedin/exome_depth_pipeline.git

3. You also need to install ExomeDepth - see the instructions for that which come with ExomeDepth.

Running

An example of running the pipeline is like this:

bpipe run -p target_bed=target_regions.bed \
          -p ref=gatk.ucsc.hg19.fasta \
          exome_depth_pipeline.groovy *.bam

Of course, you need to replace the target regions, reference fasta and BAM files with your own.

On a small target region this takes about 2 minutes to run on a moderately powerful server. If you do not have enough RAM to run all the chromosomes in parallel, you can limit throughput with -n as an argument to Bpipe.