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Get Metrics Specifications

Process Details

  • Name: getMetrics
  • Process UUID: FWCViS8QdbyDsDrU4og82E3ylOpK1K
  • Process Group: gatk4

Overview

This process collects comprehensive alignment metrics for BWA-aligned sequencing data. It performs quality assessment of deduplicated BAM files by generating alignment summary statistics, insert size metrics, and depth coverage information to evaluate the quality and characteristics of the sequencing alignment.

This process is implemented in Bash, which invokes Picard tools and Samtools for alignment quality assessment.

Key Functionality

  • Alignment Summary Metrics: Collects detailed alignment statistics including mapping rates, error rates, and quality scores using Picard CollectAlignmentSummaryMetrics
  • Insert Size Analysis: Generates insert size distribution metrics and creates histogram visualizations using Picard CollectInsertSizeMetrics
  • Depth Coverage Calculation: Computes per-base depth coverage across the genome using Samtools depth

Input/Output Specification

Inputs

Required Inputs

  • Deduplicated BAM

    • Description: Set of deduplicated BAM files from alignment processing
    • Format: BAM

  • Genome Dictionary

    • Description: Reference genome dictionary file containing sequence information
    • Format: DICT

Outputs

  • Alignment Metrics

    • Description: Text file containing alignment summary statistics and quality metrics
    • Format: TXT

  • Insert Size Metrics

    • Description: Text file containing insert size distribution statistics
    • Format: TXT

  • Insert Size Histogram

    • Description: PDF visualization of insert size distribution
    • Format: PDF

  • Depth Coverage

    • Description: Text file containing per-base depth coverage information
    • Format: TXT

Parameters & Settings

This process uses conditional execution based on the run_Metrics parameter configured at the workflow level.

References & Resources

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