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Picard MarkDuplicates Specifications

Process Details

  • Name: Picard MarkDuplicates
  • Process UUID: 20bdd3bc-ed05-11e8-9ce4-85221b21564c
  • Process Group: QC

Overview

This process identifies and tags duplicate reads in BAM files, where duplicate reads are defined as originating from a single fragment of DNA. The tool marks PCR and optical duplicates while preserving the original reads for quality control purposes. Additionally, it generates comprehensive statistics about duplicate rates and properly paired reads before and after deduplication processing.

This process is implemented in Bash, which invokes Picard tools and SAMtools for duplicate detection and BAM file processing.

Key Functionality

  • Duplicate Detection: Uses Picard MarkDuplicates to identify and tag duplicate reads based on alignment coordinates
  • Quality Control Statistics: Generates detailed flagstat reports showing duplicate rates and alignment statistics
  • BAM Processing: Removes duplicate-marked reads and sorts the resulting BAM file by chromosomal position
  • Comparative Analysis: Provides before and after deduplication statistics for quality assessment

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads
    • Description: BAM file containing aligned sequencing reads
    • Format: BAM

Outputs

  • Mapped Reads

    • Description: Processed BAM file with duplicates removed and sorted by chromosomal position
    • Format: BAM

  • Publish

    • Description: Publication-ready output files for downstream analysis
    • Format: Publish

  • Log File

    • Description: Comprehensive log containing Picard metrics, duplicate statistics, and flagstat reports before and after deduplication
    • Format: Log

Parameters & Settings

This process uses conditional execution based on pipeline configuration but does not expose user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on Picard MarkDuplicates implementation
  • Related Papers: Li, H. et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. DOI: 10.1093/bioinformatics/btp352