D3b Canine Somatic Workflow (beta)

Creating this release to mark the end of the previous efforts to create a Canine Somatic Workflow. Included in this release is a pretty interesting analysis of the padding flag on Lancet runtime, variant counts, and VAF.

What's Changed

• Lancet padding analyses by @tkoganti in #11
• 🧬 Lancet padding vaf by @tkoganti in #12
• Vep99 by @tkoganti in #13
• Updating README with VEP by @tkoganti in #14

Full Changelog: 0.1.1...v0.1.2

D3b Canine Somatic Workflow (beta) 0.1.1

Compared to version 0.1.0 -

• Removed tools that were not being used like VEP and controlfreeC

• Added consensus methods for somatic variant callers

• Updated README.md with consensus variant calling section and bcbio docker image

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.