Workflow Description

CHIP-VAR workflow consists of multiple sub-workflows, written in Common Workflow Language (CWL). Figure 1 shows the complete pipeline grouped according to functionality.

The 3 major steps in the order of working are

1. Variant Calling,

2. Variant Annotation,

3. Filtering and Tagging

The pipeline is run for every sample in a project and finally, the results from all the samples in a particular project are then combined to further filter for artifacts and likely germline variants.

This set of variants is then marked as either High Confidence [HC] CH-PD [CH Putative Driver mutations] or non-CH-PD based on the conditions listed in the white boxes.

Complete Workflow for CHIP-VAR

Variant Calling for CHIP-VAR

The bottom light pink box in the above image elaborates on the variant calling workflow using the VarDictJava tool which consists of: calling, sorting, normalizing, and concatenating the complex and normal variant VCF files.