Guide: How to Convert BAM to SAM

This guide provides a detailed explanation of BAM and SAM formats and step-by-step instructions on converting BAM to SAM using the latest tools and techniques.

What is BAM and SAM?

• SAM (Sequence Alignment/Map):
  A text-based format for storing biological sequence alignments. It contains both alignment information and sequence data in a human-readable tab-delimited format. SAM files include a header section (optional) and an alignment section.
• BAM (Binary Alignment/Map):
  A binary, compressed version of SAM designed for computational efficiency. BAM files are smaller and faster to process but are not human-readable.

Converting BAM to SAM may be necessary for debugging, data inspection, or tool compatibility.

Prerequisites

1. Install SAMtools:
   SAMtools is the most popular tool for handling SAM and BAM files. Ensure it’s installed on your system. To install:
   bash

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   sudo apt-get install samtools # For Ubuntu/Debian
brew install samtools # For macOS with Homebrew
conda install -c bioconda samtools # Using Conda

2. Verify installation:
   bash

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   samtools --version


Step-by-Step Instructions

Basic Conversion of BAM to SAM

To convert a single BAM file to a SAM file:

1. Open your terminal.
2. Run the following command:
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   samtools view -h -o output.sam input.bam

   • -h ensures the header is included in the SAM output.
   • Replace input.bam with your BAM file name and output.sam with your desired output name.

Using Redirection

Alternatively, use redirection to create the SAM file:

Batch Conversion of BAM to SAM

For multiple BAM files in a directory:

1. Navigate to the directory containing your BAM files:
   bash

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   cd /path/to/bam/files

2. Use the following for loop in UNIX shell:
   bash

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   for file in *.bam
do
echo "Processing $file..."
samtools view -h "$file" > "${file%.bam}.sam"
done


Explanation:

• *.bam selects all BAM files in the directory.
• ${file%.bam} removes the .bam extension and appends .sam.

Parallel Batch Conversion

To speed up batch processing, you can use the parallel command:

1. Install GNU Parallel if not already installed:
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   sudo apt-get install parallel # Ubuntu/Debian
brew install parallel # macOS

2. Run parallel conversion:
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   parallel --plus 'samtools view -h {} -o {...}.sam' ::: *.bam

   • --plus enables advanced argument parsing.
   • {} is replaced by each BAM file.
   • {...} removes the .bam extension.

Verification

After conversion, verify the integrity of the SAM files:

This displays the first few lines of the SAM file, including the header.

Script for Automation

If you frequently convert BAM to SAM, automate the task with a script:

1. Save this script as convert_bam_to_sam.sh.
2. Make it executable:
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   chmod +x convert_bam_to_sam.sh

3. Run the script in the directory containing your BAM files.

Using Galaxy

Galaxy provides a web-based interface for BAM-to-SAM conversion:

1. Upload your BAM file to Galaxy.
2. Search for the “SAMtools View” tool.
3. Set the output format to SAM and run the tool.

Notes

• Always include the -h flag to preserve headers.
• Keep your SAMtools version updated for compatibility with newer BAM formats:
  bash

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  samtools update

• For large datasets, use parallel for faster processing.

This guide equips you to convert BAM to SAM effectively using SAMtools, batch processing, or parallel computing.