Further Information

Detection Tools

BreakDancer	https://github.com/genome/breakdancer/
GATK/MuTect	https://software.broadinstitute.org/gatk/
GenomeSTRiP	http://software.broadinstitute.org/software/genomestrip/
Pindel	https://github.com/genome/pindel/
Strelka	https://sites.google.com/site/strelkasomaticvariantcaller/home/
VarScan	http://varscan.sourceforge.net/

Supporting Tools

bam-readcount	https://github.com/genome/bam-readcount/
Java SE Runtime Environment	http://www.oracle.com/technetwork/java/javase/downloads/
S3 Tools	http://s3tools.org/s3cmd/
SAMtools	http://www.htslib.org/
SnpEff	http://snpeff.sourceforge.net/
StarCluster	http://star.mit.edu/cluster/
Variant Effect Predictor	http://ensembl.org/info/docs/tools/vep/
VCF tools	https://vcftools.github.io/

Amazon AWS Documentation

Documentation home	https://aws.amazon.com/documentation/
EC2 home	https://aws.amazon.com/documentation/ec2/
S3 home	https://aws.amazon.com/documentation/s3/
EBS home	http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AmazonEBS.html