SAMtools

SAMtools is the toolkit for manipulating sequence alignment data in SAM, BAM and CRAM formats, and along with its sibling BCFtools and the underlying HTSlib it is the foundation almost every genomics pipeline is built on. If reads have been aligned, SAMtools has almost certainly touched the file.

What it does

It sorts, indexes, filters, merges and converts alignment files, computes coverage statistics and generates pileups for variant calling. Indexing enables random access to specific regions of enormous files without reading them end to end, which is what makes interactive genome browsing feasible. CRAM support delivers substantial storage savings over BAM.

Strengths

• Free and open source, and the de facto standard for alignment data.
• Fast C implementation that handles very large files efficiently.
• Region indexing for random access without full reads.
• CRAM compression for meaningful storage savings.
• Composes cleanly in shell pipelines.

Limitations

It is a command-line tool with terse documentation and a flag-heavy interface, and the SAM flag encoding in particular is a reliable source of quiet errors — filtering on the wrong bit silently produces a plausible but wrong result. It manipulates alignments; it does not align. Expect to consult the manual every time.