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CREST on Biowulf

CREST (Clipping Reveals Structure) is an algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data.

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

module avail CREST

To select a module, type

module load CREST/[ver]

where [ver] is the version of choice. This will set the $PATH and $PERLLIB variables, as well as $CRESTTHOME.

Submitting a single batch job

CREST requires a BLAT server, so this must be started within the job. The following qsub script will automatically start a BLAT server on the given node, and wait until it is ready for queries.

#!/bin/bash
#PBS -N CREST

cd $PBS_O_WORKDIR
module load CREST

# Start up BLAT server:
gfServer start $(hostname) 50000 $CRESTHOME/hg18.2bit -canStop -log=blatServer.log &

# Wait until the BLAT server is up and running
while [[ $(gfServer files $(hostname) 50000 2>&1) =~ "Error in TCP" ]]; do echo "Waiting for BLAT server to start..." ; sleep 10 ; done

echo "BLAT server is running!"

# Run
extractSClip.pl -i tumor.bam --ref_genome $CRESTHOME/hg18.fa
extractSClip.pl -i germline.bam --ref_genome $CRESTHOME/hg18.fa
CREST.pl -f tumor.bam.cover -d tumor.bam -g germline.bam --ref_genome $CRESTHOME/hg18.fa -t $CRESTHOME/hg18.2bit --blatserver $(hostname)

# Shut down BLAT server
echo "Shutting down BLAT server..."
gfServer stop $(hostname) 50000

Submit the script using the 'qsub' command on Biowulf

$ qsub -l nodes=1 /data/$USER/theScriptFileAbove
Documentation

CREST home at St. Jude Children's Hospital