Samtools

Samtools are a set of utilities that manipulate alignments in SAM, BAM, and CRAM file formats. It manages conversions between formats, handles sorting, merging, indexing, and can retrieve reads in any region swiftly. It treats any input as stdin and output as stdout.

tip

Several other tools load with this module. Review additional available tools using the command below:

report_subtools.sh samtools

For additional information, please see the Samtools documentation.

Parallel Capabilities: Single core only.