Skip to content

Remove Multimappers with Samtools Specifications

Process Details

  • Name: Remove_Multimappers_with_Samtools
  • Process UUID: 20bdd8ee-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process removes multi-mapped reads from BAM files to improve the quality of sequencing data analysis. Multi-mapped reads are sequences that align to multiple locations in the reference genome with similar confidence, which can introduce ambiguity in downstream analyses. The tool filters out reads based on their MAPQ (Mapping Quality) scores, retaining only uniquely mapped reads that meet the specified quality threshold.

This process is implemented in Bash, which invokes Samtools for BAM file filtering operations.

Key Functionality

  • Multi-mapper Removal: Filters out reads that map to multiple genomic locations
  • Quality-based Filtering: Removes reads with MAPQ scores below the specified threshold
  • BAM File Processing: Maintains proper BAM format and headers during filtering
  • Unique Read Retention: Preserves only high-confidence, uniquely mapped reads

Input/Output Specification

Inputs

Required Inputs

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

Outputs

  • Mapped Reads
    • Description: Filtered BAM files containing only uniquely mapped reads that meet the MAPQ quality threshold
    • Format: BAM

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • MAPQ Quality
    • Description: It removes reads with MAPQ quality less than entered value (4 by default)
    • Default value: 4

References & Resources

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