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Binary Alignment/Map (BAM)

Definition
AI-generated

BAM is the compressed binary representation of SAM records for aligned sequencing reads, designed for efficient storage, indexing, and random access.

Topics
Bioinformatics Formats
URL
https://samtools.github.io/hts-specs/SAMv1.pdf
Related
Sequence Alignment/Map (SAM) CRAM FASTQ

Why it matters in GWAS

In sequencing-based GWAS pipelines, BAM files are a core intermediate that feed variant calling and quality assessment; alignment quality directly influences downstream association validity.

Example usage

"Aligned BAM files were indexed and passed to the joint variant-calling workflow."

Sequence Alignment/Map (SAM) CRAM FASTQ Variant Calling
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Li H, et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics. https://doi.org/10.1093/bioinformatics/btp352
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