-.B import
-samtools import <in.ref_list> <in.sam> <out.bam>
-
-Since 0.1.4, this command is an alias of:
-
-samtools view -bt <in.ref_list> -o <out.bam> <in.sam>
-
-.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 [-h inh.sam] [-n] <out.bam> <in1.bam> <in2.bam> [...]
-
-Merge multiple sorted alignments.
-The header reference lists of all the input BAM files, and the @SQ headers of
-.IR inh.sam ,
-if any, must all refer to the same set of reference sequences.
-The header reference list and (unless overridden by
-.BR -h )
-`@' headers of
-.I in1.bam
-will be copied to
-.IR out.bam ,
-and the headers of other files will be ignored.
-
-.B OPTIONS:
-.RS
-.TP 8
-.B -h FILE
-Use the lines of
-.I FILE
-as `@' headers to be copied to
-.IR out.bam ,
-replacing any header lines that would otherwise be copied from
-.IR in1.bam .
-.RI ( FILE
-is actually in SAM format, though any alignment records it may contain
-are ignored.)
-.TP
-.B -n
-The input alignments are sorted by read names rather than by chromosomal
-coordinates
-.RE
-
-.TP
-.B index
-samtools index <aln.bam>
-
-Index sorted alignment for fast random access. Index file
-.I <aln.bam>.bai
-will be created.
-
-.TP