12 read order

–keepReadOrder Keep order of reads in BAM output the same as that in the input file. Reads from the same pair are always placed next to each other no matter this option is specified or not.

–sortReadsByCoordinates Output location-sorted reads. This option is applicable for BAM output only. A BAI index file is also generated for each BAM file so the BAM files can be directly loaded into a genome browser.