Skip to content

VCF Comparison Specifications

Process Details

  • Name: vcfcomparison
  • Process UUID: MpzQ9IxYvpqI37Xi6yPE4LExWVuC6g
  • Process Group: gatk4

Overview

This process performs comparative analysis of multiple VCF (Variant Call Format) files to identify shared and unique variants across different groups or samples. It enables researchers to systematically compare variant calls between different conditions, samples, or analysis methods by creating intersections and generating differential variant sets.

This process is implemented in Bash, which invokes a Perl script for VCF file processing and comparison operations.

Key Functionality

  • VCF File Grouping: Organizes input VCF files into user-defined groups based on provided grouping criteria
  • Variant Intersection Analysis: Identifies common variants within groups using vcf-isec functionality
  • Differential Variant Detection: Generates variant sets that are present in one group but absent in another
  • Tabular Output Generation: Creates TSV format files containing variant comparison results for downstream analysis

Input/Output Specification

Inputs

Required Inputs

  • Output File VCF

    • Description: Primary VCF file containing variant calls to be compared
    • Format: VCF format

  • Value Tuple

    • Description: Configuration parameters for the comparison analysis
    • Format: Value tuple

Optional Inputs

  • Groups
    • Description: Text file defining how VCF files should be grouped for comparison
    • Format: TXT format

Outputs

  • VFC File

    • Description: Variant comparison file containing intersection results
    • Format: VFC format

  • Output File TSV

    • Description: Tab-separated values file with detailed variant comparison statistics and results
    • Format: TSV format

References & Resources

  • Tool Documentation: Contact the team for details on the Perl comparison script