processing sequence alignments in SAM and BAM 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) format, 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 (not SAM) file on a remote FTP or HTTP
 server.