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Base Recalibration Specifications

Process Details

  • Name: Base Recalibration
  • Process UUID: t78wsgsqx2ehp4859lod7hxdlvx0ug
  • Process Group: gatk4

Overview

Base Recalibration is a critical preprocessing step in genomic variant calling pipelines that corrects systematic biases in base quality scores produced by sequencing machines. This process analyzes patterns of covariation among several features of a base and generates a recalibration table that can be used to adjust quality scores, ultimately improving the accuracy of variant calling.

This process is implemented in Bash, which invokes GATK4's BaseRecalibrator tool for quality score recalibration.

Key Functionality

  • Quality Score Analysis: Analyzes systematic errors in base quality scores by examining covariation patterns across multiple sequence features
  • Recalibration Table Generation: Creates a recalibration table containing empirical quality score corrections based on known variant sites
  • Systematic Bias Correction: Identifies and models machine-specific and chemistry-specific systematic biases in quality score assignment

Input/Output Specification

Inputs

Required Inputs

  • BAM File

    • Description: Aligned sequencing reads in BAM format requiring quality score recalibration
    • Format: BAM

  • Genome Dictionary

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

  • VCF Files

    • Description: Known variant sites (SNPs and indels) used as truth sets for recalibration modeling
    • Format: VCF

Outputs

  • Recalibration Table

    • Description: Text file containing base quality score recalibration data and covariation model parameters
    • Format: TXT

  • Output BAM File

    • Description: Processed BAM file ready for subsequent analysis steps
    • Format: BAM

Parameters & Settings

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

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

References & Resources

  • Tool Documentation: Contact the team for details on GATK4 BaseRecalibrator
  • 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.