SAM/BAM

Provides a format for storing next-generation sequencing read data

When sequencing DNA, the raw sequences that come off a machine — the “reads” — are aligned to a reference genome. Then, thee reads are traditionally stored in one of two file types: a human-readable text file of sequence data called SAM (Sequence Alignment/Map), and its binary counterpart, BAM (Binary Alignment/Map).

Maintained by the GA4GH Large Scale Genomics (LSG) Work Stream, SAM and BAM are used throughout the genomics and health field to store genomic sequences. The highly-compressed version of BAM, CRAM, is transitioning into the field’s preferred file format for storing sequencing reads, as it reduces file size and thus storage costs.

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Benefits

  • Provides a common format to store genomic sequence read data

Target users

Researchers, and data custodians

Image summary: Learn how the formats SAM/BAM and CRAM store aligned sequencing reads — a foundational step when working with genomic data.

Community Resources

Dive deeper into this Product!The genomics community has traditionally used SAM and BAM to store sequencing reads. In essence, SAM is a TAB-delimited text format consisting of an optional header section and an alignment section that aligns the sequences to a reference genome. Each alignment line has eleven mandatory fields for essential alignment information, such as mapping position. BAM converts this information into binary code, reducing the file size.


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Title

Info

Repeat

Day

Time

Duration

This group meets to discuss all GA4GH File Formats maintained by the Large-Scale Genomics Work Stream: SAM/BAM/CRAM and VCF/BCF.

Every Two Months
Tuesday
00:00 UTC
1 Hour

This group meets to discuss all GA4GH File Formats maintained by the Large-Scale Genomics Work Stream: SAM/BAM/CRAM and VCF/BCF.

Every Two Months
Tuesday
20:00 UTC
1 Hour
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Date

Version

22 Aug 2022
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Title

Related Driver Projects and Organisations

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  • Robert Davies
    Wellcome Sanger Institute (WSI)
  • Richard Durbin
    University of Cambridge
  • Yosr Hamdi
    Institut Pasteur de Tunis
  • Michael Hoffman
    Princess Margaret Cancer Centre
  • John Marshall
    University of Glasgow
  • Martin Pollard
    Wellcome Sanger Institute (WSI)

News, events, and more

Catch up with all news and articles associated with SAM/BAM.

8 Jul 2021
GA4GH Standards in a Global Learning Health System
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