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Mark Duplicates Specifications

Process Details

  • Name: markDuplicates
  • Process UUID: 9LlaiIIpNwvnhw11XaVPTShQ9bGhYu
  • Process Group: gatk4

Overview

This process performs duplicate removal on mapped sequencing reads using GATK's MarkDuplicates tool. Duplicate reads are identified and marked (or removed) to improve the quality of downstream variant calling and analysis by reducing PCR amplification artifacts and optical duplicates that can lead to false positive variant calls.

This process is implemented in Bash.

Key Functionality

  • Duplicate Detection: Identifies duplicate reads based on mapping coordinates and insert size
  • Metrics Generation: Produces detailed statistics about duplicate rates and library complexity
  • BAM Processing: Outputs a cleaned BAM file with duplicates marked or removed
  • Temporary File Management: Creates and manages temporary directories for intermediate processing files

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads
    • Description: Aligned sequencing reads in BAM format
    • Format: BAM

Outputs

  • Mapped Reads

    • Description: Processed BAM file with duplicate reads marked or removed
    • Format: BAM

  • Metrics File

    • Description: Text file containing duplicate marking statistics and metrics including total reads, duplicate reads, estimated library size, and duplication rates
    • Format: TXT

Parameters & Settings

This process uses default GATK MarkDuplicates parameters and does not expose user-configurable options in the Foundry UI.

References & Resources

  • Tool Documentation: GATK MarkDuplicates Documentation
  • Related Papers: McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297-303. doi:10.1101/gr.107524.110