Introducing the Cancer Genome Analysis Suite
Single nucleotide substitutions can reveal information on the root causes of cancer disease progression and differing treatment response, but they are notoriously difficult to identify. Appistry’s new Cancer Genome Analysis Suite delivers for the first time an integrated set of tools from the Broad Institute to power cancer studies. And through Appistry's relationship with the Broad, the suite will be extended to provide an end-to-end toolset for reliably and accurately calling somatic variants and indels in NGS data.
The Cancer Genome Analysis Suite includes the following tools:
- GATK, which performs indel realignment and base quality score recalibration to prepare deduplicated BAM files for calling somatic variants and indels.
- MuTect, the Broad’s tool for reliably and accurately identifying somatic point mutations in NGS data. MuTect has been proven in nearly a dozen independent studies to deliver high sensitivity while retaining specificity.
- NEW! ContEst, a tool for estimating the level of cross-individual contamination in a dataset to reduce the number of false positive calls and further improve MuTect’s specificity.
- Somatic Indel Detector, which rounds out the workflow by identifying somatic indels.
In addition to the toolset, Appistry has extended the information provided by the Broad to guide you in getting the most out of suite. Our best practices support provides
- Full documentation on using the Cancer Genome Analysis Suite for studying NGS cancer samples
- A test dataset and results summary for validating the workflow
- A Perl script with default parameters to ensure that the tools in the Cancer Genome Analysis Suite are accurately connected and configured. The script can be run across either the test dataset or a customer’s dataset, and can be modified by customers wishing to supply their own custom parameters.
Schedule a consultation now to learn more about Cancer Genome Analysis Suite!