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Deduplication Summary Specifications

Process Details

  • Name: Deduplication Summary
  • Process UUID: 17fc5d44-e169-11e9-be30-e0aab38271b1
  • Process Group: Misc.

Overview

This process parses samtools flagstat output to create a comprehensive deduplication summary table. It analyzes alignment statistics before and after deduplication to calculate duplication ratios for sequencing samples, providing essential quality control metrics for genomic data processing pipelines.

This process is implemented in Perl.

Key Functionality

  • Flagstat Parsing: Extracts alignment statistics from samtools flagstat log files
  • Deduplication Analysis: Compares read counts before and after duplicate removal
  • Summary Table Generation: Creates a TSV file with deduplication metrics for all samples
  • Paired-end Support: Handles both single-end and paired-end sequencing data appropriately

Input/Output Specification

Inputs

Required Inputs

  • Log File

    • Description: Samtools flagstat log file containing alignment statistics
    • Format: log

  • Mate

    • Description: Sequencing type specification (single-end or paired-end)
    • Format: mate

Outputs

  • Output File TSV
    • Description: Summary table containing deduplication statistics including read counts before/after deduplication and duplication ratios
    • Format: tsv

References & Resources

  • Tool Documentation: Standard samtools flagstat output parsing - contact bioinformatics team for implementation details