.BAM

Binary Alignment Map

Learn about .bam files - Binary Alignment Map. Find software to open, compatibility information, and alternatives.

Data 40 Searches File Extension Details
.BAM
Binary Alignment Map

What is a .bam file?

File Extension Details

The BAM (Binary Alignment Map) file format is the compressed binary version of the Sequence Alignment Map (SAM) format, designed specifically for storing large-scale biological sequence alignments. In the field of bioinformatics, researchers use BAM files to manage the output of sequence aligners that map raw sequencing reads—typically from Next-Generation Sequencing (NGS) platforms—to a reference genome. Because raw genomic data can be incredibly voluminous, the BAM format employs BGZF (Blocked GNU Zip Format) compression to minimize storage space while maintaining high performance. One of the most significant advantages of the BAM format is its support for indexing; when accompanied by a .bai index file, software can perform rapid random access to specific genomic coordinates without needing to parse the entire dataset. Each record in a BAM file includes the read name, sequence, quality scores, mapping position, and a CIGAR string representing the alignment's structural details. This format is essential for downstream analysis tasks, including variant calling, structural variation detection, and visualization in genome browsers, making it a cornerstone of modern genomic research.

Software Compatibility

Programs that can open and work with .bam files

Windows

Compatible Applications

IGV (Integrative Genomics Viewer) Compatible
Tablet Compatible
Samtools (via WSL) Compatible
Golden Helix GenomeBrowse Compatible

macOS

Compatible Applications

IGV (Integrative Genomics Viewer) Compatible
Samtools Compatible
Integrated Genome Browser (IGB) Compatible
BamView Compatible

Linux

Compatible Applications

Samtools Compatible
BCFtools Compatible
GATK (Genome Analysis Toolkit) Compatible
Picard Tools Compatible
BWA (Burrows-Wheeler Aligner) Compatible
IGV Compatible

Mobile

Mobile Applications

IGV-Web (Browser-based) Compatible
JBrowse 2 (Web-based) Compatible

Frequently Asked Questions

About .bam files

To open a .bam file, you need compatible software. Here are some options:

  • IGV (Integrative Genomics Viewer)
  • Tablet
  • Samtools
  • IGV-Web (Browser-based)

To convert a .bam file to another format, you can:

  1. Use compatible software Many programs that open .bam files also allow you to save or export them to different formats.
  2. Try online conversion services: Websites like Zamzar, CloudConvert, or Online-Convert allow you to convert files between different formats without installing software.
  3. Specialized conversion tools: Search for '.bam converter' to find tools specifically designed for this file type.

  1. Verify the file extension is correct:
  2. Update your software:
  3. Try alternative software:
  4. Check for file corruption:

Like any file type, .bam files can be safe or potentially risky depending on their source:

  • Always scan files with antivirus software before opening
  • Keep your operating system and applications updated.
  • Be especially cautious with executable file types

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