What it does

The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to.

Coordinate-sorted input files are expected by most downstream MiModD tools, but note that the SNAP Read Alignment produces coordinate-sorted output by default and it is only necessary to sort files that come from other sources or from SNAP Read Alignment jobs with a custom sort order.

The option Sort by read names instead of coordinates is useful if you want to re-align coordinate-sorted paired-end data. In paired-end mode, the SNAP Read Alignment tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem.