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Bam Sort Index Specifications

Process Details

  • Name: bam_sort_index
  • Process UUID: pgf34oef0xvl0xqe4mso6z9o7filx8
  • Process Group: Misc.

Overview

This process sorts BAM alignment files and creates corresponding index files, returning a tuple containing the sample name, sorted BAM file, and BAI index file. The process is essential for downstream analyses that require sorted and indexed BAM files, such as visualization in genome browsers, variant calling, and quality control assessments.

This process is implemented in Bash.

Key Functionality

  • BAM File Sorting: Sorts BAM files using samtools sort to organize alignments by genomic coordinates
  • Index Generation: Creates BAI index files using samtools index for rapid random access to alignment data
  • Conditional Processing: Intelligently detects if BAM files are already sorted to avoid redundant processing
  • File Organization: Organizes output files into a dedicated directory structure for downstream processing

Input/Output Specification

Inputs

Required Inputs

  • Mapped Reads
    • Description: BAM alignment files containing mapped sequencing reads
    • Format: BAM

Outputs

  • BAM BAI
    • Description: Sorted BAM files with corresponding BAI index files packaged as a tuple
    • Format: BAM_BAI

Parameters & Settings

This process runs conditionally when BigWig conversion or RSeQC analysis is enabled in the pipeline configuration.

References & Resources

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