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CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. CONTRA calls copy number gains and losses for each target region with key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. It takes standard alignment formats (BAM/SAM) and output in variant call format (VCF 4.0) for easy integration with other next generation sequencing analysis package.

How to Use

There are multiple versions of CONTRA available. An easy way of selecting the version is to use modules. To see the versions available, type

module avail CONTRA

To select a version, type

module load CONTRA/[ver]

where [ver] is the version of choice.


Create a qsub script (e.g. contra.qsub),

# ----  this file is called contra.qsub ---------

module load CONTRA 2>&1
  -t /path/to/bed.file \
  -s /path/to/test.bam \
  -c /path/to/control.bam \
  -f /path/to/reference.fasta \
  -o /path/to/output.folder

modify the bolded paths, and submit it like so:

qsub -l nodes=1:c4 control.qsub

This example assumes that only 8 GB of memory is required. Please use jobload to monitor your memory usage.


If there are multiple sets of alignments, CONTRA can be run as a swarm. Create a swarmfile (e.g. contra.swarm),

again after modifying the paths as with qsub, and submit it like so:

swarm --module CONTRA -g 8 -f contra.swarm