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BaseRecalibrator Specifications

Process Details

  • Name: BaseRecalibrator
  • Process UUID: mOCtbaNK8wc2jriEJcKwen5vgR9U7g
  • Process Group: gatk4

Overview

BaseRecalibrator performs Base Quality Score Recalibration (BQSR) to detect and correct systematic errors in base quality scores assigned by sequencing machines. This process improves the accuracy of variant calling by recalibrating quality scores based on empirical data from known variant sites. BQSR is performed twice in this implementation, with the second pass being optional and used primarily to produce a recalibration report for quality assessment.

This process is implemented in Bash, which invokes GATK4 tools for variant selection and base quality score recalibration.

Key Functionality

  • Variant Selection: Filters and selects high-quality SNPs and indels from input VCF files to serve as known sites for recalibration
  • Base Quality Recalibration: Analyzes patterns of covariation in quality scores and generates recalibration tables to correct systematic biases
  • Quality Score Correction: Produces recalibrated BAM files with improved base quality scores for downstream variant calling

Input/Output Specification

Inputs

Required Inputs

  • VCFset

    • Description: Set of VCF files containing filtered variants (SNPs and indels) to be used as known sites for recalibration
    • Format: VCF

  • genomeDict

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

Outputs

  • VCFset

    • Description: Processed VCF files with selected variants used for base recalibration
    • Format: VCF

  • run_parameters

    • Description: Runtime parameters and configuration settings used during the recalibration process
    • Format: run_parameters

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Optional gatk BaseRecalibrator parameters
    • Description: Optional gatk BaseRecalibrator parameters
    • Default value: "" (empty string)

References & Resources

  • Tool Documentation: GATK4 BaseRecalibrator 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