3 input reads and output

-o Name of an output file. By default, the output is in BAM format. Omitting this option makes the output be written to STDOUT.

-R Name of the second read file in paired-end data (typically containing “R2” the file name).

–SAMinput Input reads are in SAM format.

–BAMinput Input reads are in BAM format.

–SAMoutput Save mapping results in SAM format.