About us
Learn how GA4GH helps expand responsible genomic data use to benefit human health.
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.
THEME
CATEGORY
TYPE
STATUS
Work Stream
LATEST VERSION
Product Lead
- James Bonfield
Staff Contact
Tools & Platforms
Publications
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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Date
Title
11 Mar 2023
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Australian Genomics
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Don't see your name? Fill out our form:
- 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)
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Catch up with all news and articles associated with SAM/BAM.
