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HaplotypeCaller Specifications

Process Details

  • Name: HaplotypeCaller
  • Process UUID: cqOz0hoY6f0WPv0wZQzjPpvivIxCq1
  • Process Group: gatk4

Overview

HaplotypeCaller performs the first and second round of variant calling in genomic data analysis pipelines. This process identifies variants from mapped sequencing reads, which will subsequently be filtered and used as input for Base Quality Score Recalibration (BQSR). The process generates raw variant calls for samples in VCF format, providing essential data for downstream variant analysis and quality control procedures.

This process is implemented in Bash, utilizing GATK's HaplotypeCaller algorithm within a containerized environment.

Key Functionality

  • Variant Detection: Identifies single nucleotide polymorphisms (SNPs) and insertion/deletion variants (indels) from aligned sequencing reads
  • BAM File Processing: Automatically indexes input BAM files and processes mapped reads against the reference genome
  • Raw Variant Output: Generates unfiltered variant calls in standard VCF format for subsequent quality control and filtering steps

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads

    • Description: Set of BAM files containing aligned sequencing reads
    • Format: BAM

  • Genome Dictionary

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

  • Round Batch Algorithm

    • Description: Algorithm configuration parameter specifying the variant calling round and batch processing settings
    • Format: roundBatchAlgorithm

Outputs

  • VCF Set
    • Description: Set of Variant Call Format files containing raw variant calls identified from the input reads
    • Format: VCF

Parameters & Settings

This process uses containerized GATK with predefined parameters. The variant calling round is determined by the roundBatchAlgorithm input parameter.

References & Resources

  • Tool Documentation: GATK HaplotypeCaller Documentation
  • 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. DOI: 10.1101/gr.107524.110