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Merge Bam and sort index Specifications

Process Details

  • Name: Merge Bam and sort index
  • Process UUID: hBX0ujWgLhQ4fR20KLXQQTdcJ42wlC
  • Process Group: Misc.

Overview

This process consolidates multiple BAM files into a single merged file, followed by sorting and indexing operations. It handles both single and multiple input BAM files, automatically determining the appropriate workflow based on the number of input files. The process is designed to prepare aligned sequencing data for downstream analysis by creating properly sorted and indexed BAM files.

This process is implemented in Bash, utilizing SAMtools for BAM file manipulation operations.

Key Functionality

  • BAM File Merging: Combines multiple BAM files into a single consolidated file when multiple inputs are provided
  • Sorting: Performs coordinate-based sorting of BAM files to ensure proper ordering for downstream applications
  • Indexing: Creates BAM index files (.bai) to enable rapid random access to specific genomic regions

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads

    • Description: Set of aligned sequencing reads in BAM format
    • Format: BAM

  • Mate

    • Description: Mate pair information for paired-end sequencing data
    • Format: mate

Outputs

  • BAM Index

    • Description: Index file enabling rapid access to specific regions in the sorted BAM file
    • Format: BAI

  • BAM File

    • Description: Merged, sorted BAM file containing all input aligned reads
    • Format: BAM

Parameters & Settings

This process does not expose user-configurable parameters in the Foundry UI. All operations are performed with default SAMtools settings.

References & Resources

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