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Select Variants Specifications

Process Details

  • Name: selectVariants
  • Process UUID: qd2625Ou7qGZ8NfCjyh6XxtBr2xx9B
  • Process Group: gatk4

Overview

This process separates SNPs and Indels from a variant call format (VCF) file so they can be processed and analyzed independently. This separation is essential for downstream variant filtering and quality control, as SNPs and Indels have different characteristics and require different filtering criteria for optimal results.

This process is implemented in Bash, which invokes GATK4's SelectVariants tool for variant type separation.

Key Functionality

  • Variant Type Separation: Splits input VCF files into separate files containing only SNPs or only Indels
  • Reference-Based Processing: Uses genome reference dictionary for proper variant calling context
  • Quality Preservation: Maintains all variant annotations and quality metrics during separation
  • Parallel Processing: Generates both SNP and Indel files simultaneously from the same input

Input/Output Specification

Inputs

Required Inputs

  • VCFset

    • Description: Variant call format files containing mixed SNPs and Indels to be separated
    • Format: VCF format

  • genomeDict

    • Description: Genome reference dictionary file providing sequence information for variant processing
    • Format: DICT format

Outputs

  • VCFset
    • Description: Separated variant files - one containing only SNPs and another containing only Indels
    • Format: VCF format

Parameters & Settings

This process uses fixed parameters optimized for variant separation and does not expose user-configurable settings in the Foundry UI.

References & Resources

  • Tool Documentation: GATK4 SelectVariants 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