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Picard Summary Specifications

Process Details

  • Name: Picard Summary
  • Process UUID: 17fc4d0e-e169-11e9-be30-e0aab38271b1
  • Process Group: QC

Overview

This process generates comprehensive summary statistics and histograms from various Picard output files, consolidating quality control metrics across multiple samples. It processes different types of Picard metrics including RNA-seq metrics, alignment summaries, base distribution cycles, insert size measurements, and quality distributions, creating unified summary files for downstream analysis and visualization.

This process is implemented in Perl.

Key Functionality

  • Metrics Consolidation: Aggregates multiple Picard output files into unified summary tables for easy comparison across samples
  • Statistical Summary Generation: Creates TSV files containing metrics such as CollectRnaSeqMetrics, alignment_summary_metrics, base_distribution_by_cycle_metrics, insert_size_metrics, quality_by_cycle_metrics, and quality_distribution_metrics
  • Histogram Processing: Extracts and consolidates histogram data from Picard outputs for visualization purposes
  • File Organization: Automatically moves generated PDF files into a dedicated "results" directory for organized output structure

Input/Output Specification

Inputs

Required Inputs

  • Picard Output Files

    • Description: Various Picard tool output files containing metrics and statistics
    • Format: .out files

  • Mate Information

    • Description: Sample mate pair information for processing paired-end sequencing data
    • Format: mate value

  • PDF Reports

    • Description: Picard-generated PDF visualization files
    • Format: PDF files

Outputs

  • Summary Statistics

    • Description: Consolidated TSV files containing metrics summaries across all samples for each Picard tool type
    • Format: TSV files

  • Organized PDF Reports

    • Description: Picard-generated PDF files organized in a results directory
    • Format: PDF files in results directory

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on the Perl summary script
  • Related Papers: Picard Tools. Broad Institute. https://broadinstitute.github.io/picard/