Kids First Data Resource Center Germline Variant Workflows

This repository contains Germline Workflows used for the Kids First Data Resource Center (DRC).

Germline Variant Workflow

The preeminent workflow in this repository is the Germline Variant Caller Workflow. This all encompassing workflow takes an input BAM/CRAM file and runs all of our production-level calling workflows on it. It will call copy number (CNV), single nucleotide (SNV), and structural variants (SV). Annotation is run on the outputs of the SNV and SV callers.

Complete documentation can be found for the main workflow an its subworkflows here:

• Germline Variant Workflow
  • CNV Variant Workflow
  • SNV Variant Workflow
    • Leverages the git submodule kf-annotation-tools for variant annotation with VEP 105 and gnomAD
    • Details linked in the readme.
  • SV Variant Workflow

Other Workflows

While not in our Germline Variant workflow, other workflows potentially useful for germline calling can be found in this repository:

• Smoove/Lumpy
• CNVkit