-.TP 10
-.B import
-samtools import <in.ref_list> <in.sam> <out.bam>
-
-Convert alignments in SAM format to BAM format. File
-.I <in.ref_list>
-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. File
-.I <in.sam>
-can be optionally compressed by zlib or gzip. A single hyphen is
-recognized as stdin or stdout, depending on the context. 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 sort
-samtools sort [-n] [-m maxMem] <in.bam> <out.prefix>
-
-Sort alignments by leftmost coordinates. File
-.I <out.prefix>.bam
-will be created. This command may also create temporary files
-.I <out.prefix>.%d.bam
-when the whole alignment cannot be fitted into memory (controlled by
-option -m).
-
-.B OPTIONS:
-.RS
-.TP 8
-.B -n
-Sort by read names rather than by chromosomal coordinates
-.TP
-.B -m INT
-Approximately the maximum required memory. [500000000]
-.RE
-
-.TP
-.B merge
-samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]
-
-Merge multiple sorted alignments. The header of
-.I <in1.bam>
-will be copied to
-.I <out.bam>
-and the headers of other files will be ignored.
-
-.B OPTIONS:
-.RS
-.TP 8
-.B -n
-The input alignments are sorted by read names rather than by chromosomal
-coordinates
-.RE