github.com/sevenbridges-openworkflows/Broad-Best-Practice-Data-pre-processing-CWL1.0-workflow-GATK-4.1.0.0/GATK_4_1_0_0_data_pre_processing_workflow

BROAD Best Practice Data Pre-processing Workflow 4.1.0.0 is used to prepare data for variant calling analysis.

It can be divided into two major segments: alignment to reference genome and data cleanup operations that correct technical biases [1].

A list of all inputs and parameters with corresponding descriptions can be found at the bottom of this page.

Common Use Cases

  • BROAD Best Practice Data Pre-processing Workflow 4.1.0.0 is designed to operate on individual samples.

This is a companion discussion topic for the original entry at github.com/sevenbridges-openworkflows/Broad-Best-Practice-Data-pre-processing-CWL1.0-workflow-GATK-4.1.0.0/GATK_4_1_0_0_data_pre_processing_workflow