D3b Canine Somatic Workflow (beta)

This is a somatic calling workflow with the help of our collaborators at TGEN and the Broad Institute. Briefly, using the ENSEMBL v86 CanFam3.1 reference, we performs somatic calling using Strelka2, Mutect2, Lancet, and VarDict Java, copy number is CNVkit, and sutrcutral variants using manta. Simple variant calls are annotated using snpEff. This is a port of the Kids First Data Resource Center Somatic Workflow and is a work in progress as we plan to use more updated references and fine-tune performance.