+.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.
+.TP
+.B -h
+Include the header in the output.
+.TP
+.B -H
+Output the header only.
+.TP
+.B -S
+Input is in SAM. If @SQ header lines are absent, the
+.B `-t'
+option is required.
+.TP
+.B -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 -o FILE
+Output file [stdout]
+.TP
+.B -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
+.B -F INT
+Skip alignments with bits present in INT [0]
+.TP
+.B -q INT
+Skip alignments with MAPQ smaller than INT [0]
+.TP
+.B -l STR
+Only output reads in library STR [null]
+.TP
+.B -r STR
+Only output reads in read group STR [null]