Sorting
The map/align system produces a BAM file sorted by reference sequence and position by default. Creating this BAM file typically eliminates the requirement to run samtools sort or any equivalent postprocessing command. To enable or disable the creation of the BAM file, you can use the ‑‑enable-sort option as follows.
| • | To enable, set to true. |
| • | To disable, set to false. |
On the reference hardware system, running with sort enabled increases the run time for a 30x full genome by about 6–7 minutes.
