.TP
.B sort
-samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
+samtools sort [-nof] [-m maxMem] <in.bam> <out.prefix>
Sort alignments by leftmost coordinates. File
.I <out.prefix>.bam
.B -n
Sort by read names rather than by chromosomal coordinates
.TP
+.B -f
+Use
+.I <out.prefix>
+as the full output path and do not append
+.I .bam
+suffix.
+.TP
.BI -m \ INT
Approximately the maximum required memory. [500000000]
.RE