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Prepare Comparisons Specifications

Process Details

  • Name: prepare_comparisons
  • Process UUID: tzvdwxdilr7seuzozrzifaafyi200g
  • Process Group: gatk4

Overview

This process prepares comparison groups and configurations for downstream genomic analysis workflows. It processes BAM files and TSV metadata to organize samples into appropriate comparison groups for statistical analysis.

This process is implemented in Bash, which invokes a Python script for comparison group preparation and configuration.

Key Functionality

  • Group Organization: Processes sample metadata to define comparison groups based on experimental conditions
  • Comparison Setup: Configures pairwise or multi-group comparisons for statistical analysis
  • Directory Structure: Creates organized directory structure for downstream analysis processes

Input/Output Specification

Inputs

Required Inputs

  • BAM File

    • Description: Binary Alignment Map file containing aligned sequencing reads
    • Format: BAM

  • Input TSV File

    • Description: Tab-separated values file containing sample metadata and group assignments
    • Format: TSV

Outputs

  • Input Directory
    • Description: Organized directory structure containing prepared comparison configurations and sample groupings
    • Format: Directory

References & Resources

  • Tool Documentation: Contact the team for details on prepare_comparisons.py