Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.
bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>
OPTIONS:
-n INT Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]
-r STR Specify the read group in a format like ‘@RG\tID:foo\tSM:bar’. [null]