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Get Metrics Specifications

Process Details

  • Name: Get Metrics
  • Process UUID: FWCViS8QdbyDsDrU4og82E3ylOpK1K
  • Process Group: gatk4

Overview

This process collects comprehensive alignment metrics for BWA-aligned BAM files to assess sequencing and alignment quality. It generates alignment summary statistics, insert size distributions, and depth coverage metrics to provide a complete quality assessment of the sequencing data.

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 read quality metrics using Picard CollectAlignmentSummaryMetrics
  • Insert Size Analysis: Calculates insert size distributions and generates histogram visualizations using Picard CollectInsertSizeMetrics
  • Coverage Depth Analysis: Computes per-base coverage depth across the genome using samtools depth

Input/Output Specification

Inputs

Required Inputs

  • Deduplicated BAM

    • Description: Deduplicated and sorted BAM file from BWA alignment
    • Format: BAM file

  • Genome Dictionary

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

Outputs

  • Alignment Metrics

    • Description: Comprehensive alignment summary statistics including mapping rates and quality metrics
    • Format: TXT file

  • Insert Size Metrics

    • Description: Insert size distribution statistics for paired-end sequencing data
    • Format: TXT file

  • Insert Size Histogram

    • Description: Visual representation of insert size distribution
    • Format: PDF file

  • Coverage Depth

    • Description: Per-base coverage depth across all genomic positions
    • Format: TXT file

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