Skip to content

Sequence Alignment/Map (SAM)

Definition
AI-generated

SAM is the text specification for records of aligned sequencing reads: each line typically describes one read’s mapping position, CIGAR string, mate pair, flags, and optional typed fields (tags).

Topics
Bioinformatics Formats
URL
https://samtools.github.io/hts-specs/SAMv1.pdf
Related
Binary Alignment/Map (BAM) CRAM Read

Why it matters in GWAS

Downstream variant calling, QC, and duplicate marking consume SAM-equivalent records (usually via BAM or CRAM); understanding flags, CIGAR, and tags is necessary to interpret alignment artifacts that propagate into genotype calls used in association studies.

Example usage

"Reads were written to coordinate-sorted SAM for debugging before converting to indexed BAM for HaplotypeCaller."

Binary Alignment/Map (BAM) CRAM Read Read mapping Soft clipping
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
← Scalable and Accurate Implementation of Generalized Mixed Model (SAIGE) Sample Missingness →

Last updated (UTC · Git history)