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Samtools Specifications

Process Details

  • Name: Samtools
  • Process UUID: f931gz0q3km6fhv830nwczfwyeqaru
  • Process Group: Misc.

Overview

This process provides various functions for genome investigation using SAMtools version 1.20. It processes SAM alignment files along with reference FASTA sequences to generate sorted and indexed BAM files for downstream genomic analysis. The process is designed to handle sequence alignment data conversion, sorting, and indexing operations essential for genomic workflows.

This process is implemented in Bash, utilizing the SAMtools suite of tools for sequence alignment manipulation.

Key Functionality

  • SAM to BAM Conversion: Converts SAM format alignment files to binary BAM format using reference genome sequences
  • BAM Sorting: Sorts BAM files by genomic coordinates for efficient downstream processing and visualization
  • BAM Indexing: Creates index files for sorted BAM files to enable rapid random access to alignment data

Input/Output Specification

Inputs

Required Inputs

  • SAM File

    • Description: Sequence alignment file containing mapped reads in SAM format
    • Format: SAM

  • FASTA File

    • Description: Reference genome sequence file used for alignment conversion
    • Format: FASTA

Outputs

  • Output Directory

    • Description: Directory containing processed BAM files, sorted BAM files, index files, and reference sequences
    • Format: Directory

  • Log Output

    • Description: Process execution log containing file paths, processing steps, and directory listings
    • Format: OUT

References & Resources

  • Tool Documentation: SAMtools official documentation available at http://www.htslib.org/doc/samtools.html
  • Related Papers: Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-2079. doi:10.1093/bioinformatics/btp352