From the documentation:
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
CyVerse UK provides the following SAMtools applications:
- convert SAM to sorted BAM
- index BAM file
- index BAM file and get stats
- sort BAM
- index FASTA file
See the official website for more details.