+.TP
+.B fixmate
+samtools fixmate <in.nameSrt.bam> <out.bam>
+
+Fill in mate coordinates, ISIZE and mate related flags from a
+name-sorted alignment.
+
+.TP
+.B rmdup
+samtools rmdup <input.srt.bam> <out.bam>
+
+Remove potential PCR duplicates: if multiple read pairs have identical
+external coordinates, only retain the pair with highest mapping quality.
+This command
+.B ONLY
+works with FR orientation and requires ISIZE is correctly set.
+
+.RE
+
+
+.SH SAM FORFAM
+
+SAM is TAB-delimited. Apart from the header lines, which are started
+with the `@' symbol, each alignment line consists of:
+
+.TS
+center box;
+cb | cb | cb
+n | l | l .
+Col Field Description
+_
+1 QNAME Query (pair) NAME
+2 FLAG bitwise FLAG
+3 RNAME Reference sequence NAME
+4 POS 1-based leftmost POSition/coordinate of clipped sequence
+5 MAPQ MAPping Quality (Phred-scaled)
+6 CIAGR extended CIGAR string
+7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
+8 MPOS 1-based Mate POSistion
+9 ISIZE Inferred insert SIZE
+10 SEQ query SEQuence on the same strand as the reference
+11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
+12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
+.TE
+
+.PP
+Each bit in the FLAG field is defined as:
+
+.TS
+center box;
+cb | cb
+l | l .
+Flag Description
+_
+0x0001 the read is paired in sequencing
+0x0002 the read is mapped in a proper pair
+0x0004 the query sequence itself is unmapped
+0x0008 the mate is unmapped
+0x0010 strand of the query (1 for reverse)
+0x0020 strand of the mate
+0x0040 the read is the first read in a pair
+0x0080 the read is the second read in a pair
+0x0100 the alignment is not primary
+0x0200 the read fails platform/vendor quality checks
+0x0400 the read is either a PCR or an optical duplicate
+.TE
+