Comments (2)
The most time-consuming part is the high-depth region, especially, tandem repeats. With option "-M" (maximum depth in a region) set up to a smaller value (e.g. 10 times the average depth), we get the speed of 1.8s/genotype.
I remember the default "-M" is probably set at a high value.
from paragraph.
I added some explanation in v2.3 README for this run time issue.
In general, from our experiments in manuscript, high-depth regions consume the majority of running time, and the result from such repetitive regions are error-prone. For now, I'd recommend skipping them by setting "-M".
We're working on better methods to correctly genotype such repeats. Hopefully, it will be public in the next few months.
Let me know if you still have running time issue by setting "-M" option to 20x depth.
from paragraph.
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from paragraph.