Hi Prachiti,
if you want to output discordant pairs, you can reduce --outFilterScoreMinOverLread and --outFilterMatchNminOverLread to below 0.5, e.g.:
--outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4
Such alignments will have 0x2, 0x4 and 0x8 bits *not* set in the FLAG field of the SAM/BAM files.
Cheers
Alex