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Analyze Covariates Specifications

Process Details

  • Name: Analyze Covariates
  • 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 statistics to generate quality control plots that help assess the effectiveness of the BQSR process in variant calling workflows.

This process is implemented in Bash, which invokes GATK4's AnalyzeCovariates tool for generating recalibration comparison reports.

Key Functionality

  • Recalibration Comparison: Analyzes differences between pre- and post-recalibration base quality scores
  • Quality Control Visualization: Generates comprehensive plots showing the impact of base quality score recalibration
  • Statistical Assessment: Provides quantitative metrics on recalibration effectiveness across different sequence contexts

Input/Output Specification

Inputs

Required Inputs

  • outputFileTab
    • Description: Tabular data containing recalibration statistics from BQSR runs
    • Format: TAB

Outputs

  • outputFilePdf
    • Description: PDF report containing recalibration plots and quality metrics comparing before and after BQSR statistics
    • Format: PDF

References & Resources

  • Tool Documentation: GATK4 AnalyzeCovariates - https://gatk.broadinstitute.org/hc/en-us/articles/360037593511-AnalyzeCovariates
  • Related Papers: McKenna, A., et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297-1303.