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Analyze Covariates Specifications

Process Details

  • Name: AnalyzeCovariates
  • Process UUID: 5ZDZTeFvyxVEfL8GjGSbwpCPldEdDi
  • Process Group: gatk4

Overview

This process produces a recalibration report based on the output from two Base Quality Score Recalibration (BQSR) runs. It compares the before and after recalibration tables to generate comprehensive plots that visualize the effectiveness of the base quality score recalibration process, which is essential for improving variant calling accuracy.

This process is implemented in Bash, which invokes GATK4's AnalyzeCovariates tool for generating recalibration quality assessment plots.

Key Functionality

  • Recalibration Assessment: Compares base quality scores before and after BQSR to evaluate recalibration effectiveness
  • Quality Visualization: Generates comprehensive PDF plots showing quality score distributions and covariate effects
  • BQSR Validation: Provides visual confirmation that the recalibration process has improved base quality score accuracy

Input/Output Specification

Inputs

Required Inputs

  • outputFileTab
    • Description: Tabular recalibration data containing before and after BQSR statistics
    • Format: tab

Outputs

  • outputFilePdf
    • Description: PDF report containing recalibration plots and quality assessment visualizations
    • Format: pdf

Parameters & Settings

This process uses default GATK4 AnalyzeCovariates parameters and does not expose user-configurable settings in the Foundry UI.

References & Resources

  • Tool Documentation: GATK4 AnalyzeCovariates Documentation
  • Related Papers: McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303. doi:10.1101/gr.107524.110