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Dec 2018 Release of Getz Lab's WES Characterization Pipeline
In December 2018 the Getz Lab published in the FireCloud Method Repository its CGA WES Characterization Workflow for the identification of somatic variants (SNVs, INDELs, CNVs) in tumor-normal paired WES data. Accompanying the workflow is a detailed user guide.
The workflow has undergone extensive testing and benchmarking, and is what the Getz Lab currently relies on for the characterization of a tumor sample through contrastive analyses of paired tumor/normal hg19 bams.
While the Getz Lab makes no commitment to provide user support for this or any of its other published workflows, we will be monitoring this Cancer Genome Analysis category of the FireCloud Forum and do are best to respond to user questions.
We expect to be updating this workflow on a regular basis (to address bug reports and make improvements that address our lab's needs).