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Merge Bam Specifications

Process Details

  • Name: Merge Bam
  • Process UUID: 20bdc5ca-ed05-11e8-9ce4-85221b21564c
  • Process Group: Misc.

Overview

This process merges multiple BAM files into a single consolidated file using samtools merge. When multiple input BAM files are provided, the process performs merging followed by sorting and indexing of the resulting BAM file. For single input BAM files, it directly performs sorting and indexing operations to ensure proper file organization for downstream analysis.

This process is implemented in Bash.

Key Functionality

  • BAM File Merging: Combines multiple BAM files into a single consolidated alignment file using samtools merge
  • Automatic Sorting: Sorts the merged or single BAM file by genomic coordinates using samtools sort
  • Index Generation: Creates BAM index files (.bai) for efficient random access to alignment data

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads
    • Description: One or more BAM files containing aligned sequencing reads
    • Format: BAM (Binary Alignment/Map format)

Outputs

  • Merged Bams

    • Description: Consolidated BAM file(s) containing all input alignments
    • Format: BAM

  • Bam Index

    • Description: Index files for efficient access to BAM data
    • Format: BAI (BAM index)

  • Sorted Bam

    • Description: Coordinate-sorted BAM file ready for downstream analysis
    • Format: BAM

Parameters & Settings

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

References & Resources

  • Tool Documentation: samtools documentation available at http://www.htslib.org/doc/samtools.html