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. The ‑‑enable-sort option can be used to enable or disable creation of the BAM file, as follows:

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To enable, set to true.

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To disable, set to false.

On the reference hardware system, running with sort enabled increases run time for a 30x full genome by about 6–7 minutes.