processing sequence alignments in SAM, BAM and CRAM formats

 Samtools is a set of utilities that manipulate nucleotide sequence alignments
 in the binary BAM format. It imports from and exports to the ascii SAM
 (Sequence Alignment/Map) and CRAM formats, does sorting, merging and indexing,
 and allows one to retrieve reads in any regions swiftly. It is designed to work
 on a stream, and is able to open a BAM or CRAM (not SAM) file on a remote FTP
 or HTTP server.