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BQSR Specifications

Process Details

  • Name: BQSR
  • Process UUID: r5biijcp3ajevlsvq8u9ybpp2jbg38
  • Process Group: gatk4

Overview

BQSR (Base Quality Score Recalibration) is a genomic data processing step that corrects systematic biases in base quality scores from sequencing data. This process applies previously calculated recalibration parameters to adjust quality scores in BAM files, improving the accuracy of downstream variant calling and analysis.

This process is implemented in Bash, which invokes GATK's ApplyBQSR tool for base quality score recalibration.

Key Functionality

  • Base Quality Recalibration: Applies systematic corrections to base quality scores based on empirical recalibration data
  • BAM File Processing: Processes aligned sequencing data while maintaining proper formatting and metadata
  • Index Generation: Automatically generates BAM index files for efficient downstream access

Input/Output Specification

Inputs

Required Inputs

  • BAM File

    • Description: Aligned sequencing data file containing reads to be recalibrated
    • Format: BAM

  • Genome Dictionary

    • Description: Reference genome dictionary file containing sequence information and metadata
    • Format: DICT

  • Input File Text

    • Description: Recalibration table containing base quality score correction parameters
    • Format: TXT

Outputs

  • BAM File
    • Description: Recalibrated BAM file with corrected base quality scores and corresponding index
    • Format: BAM

Parameters & Settings

This process uses fixed parameters optimized for standard BQSR workflows. No user-configurable parameters are available in the Foundry UI.

References & Resources

  • Tool Documentation: GATK ApplyBQSR Documentation
  • Related Papers: McKenna, A., Hanna, M., Banks, E., et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297-1303. DOI: 10.1101/gr.107524.110