+.B view
+samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]]
+
+Extract/print all or sub alignments in SAM or BAM format. If no region
+is specified, all the alignments will be printed; otherwise only
+alignments overlapping the specified regions will be output. An
+alignment may be given multiple times if it is overlapping several
+regions. A region can be presented, for example, in the following
+format: `chr2' (the whole chr2), `chr2:1000000' (region starting from
+1,000,000bp) or `chr2:1,000,000-2,000,000' (region between 1,000,000 and
+2,000,000bp including the end points). The coordinate is 1-based.
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -b
+Output in the BAM format.
+.TP
+.BI -f \ INT
+Only output alignments with all bits in INT present in the FLAG
+field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]
+.TP
+.BI -F \ INT
+Skip alignments with bits present in INT [0]
+.TP
+.B -h
+Include the header in the output.
+.TP
+.B -H
+Output the header only.
+.TP
+.BI -l \ STR
+Only output reads in library STR [null]
+.TP
+.BI -o \ FILE
+Output file [stdout]
+.TP
+.BI -q \ INT
+Skip alignments with MAPQ smaller than INT [0]
+.TP
+.BI -r \ STR
+Only output reads in read group STR [null]
+.TP
+.BI -R \ FILE
+Output reads in read groups listed in
+.I FILE
+[null]
+.TP
+.B -S
+Input is in SAM. If @SQ header lines are absent, the
+.B `-t'
+option is required.
+.TP
+.B -c
+Instead of printing the alignments, only count them and print the
+total number. All filter options, such as
+.B `-f',
+.B `-F'
+and
+.B `-q'
+, are taken into account.
+.TP
+.BI -t \ FILE
+This file is TAB-delimited. Each line must contain the reference name
+and the length of the reference, one line for each distinct reference;
+additional fields are ignored. This file also defines the order of the
+reference sequences in sorting. If you run `samtools faidx <ref.fa>',
+the resultant index file
+.I <ref.fa>.fai
+can be used as this
+.I <in.ref_list>
+file.
+.TP
+.B -u
+Output uncompressed BAM. This option saves time spent on
+compression/decomprssion and is thus preferred when the output is piped
+to another samtools command.
+.RE
+
+.TP
+.B tview
+samtools tview <in.sorted.bam> [ref.fasta]
+
+Text alignment viewer (based on the ncurses library). In the viewer,
+press `?' for help and press `g' to check the alignment start from a
+region in the format like `chr10:10,000,000' or `=10,000,000' when
+viewing the same reference sequence.
+
+.TP
+.B mpileup
+samtools mpileup [-Bug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]