MantaMerger running time too long and potential speeding up methods?

lindenb / jvarkit

Java utilities for Bioinformatics

https://jvarkit.readthedocs.io/

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MantaMerger running time too long and potential speeding up methods? #173

Closed zjgbz closed 7 months ago

zjgbz commented 3 years ago

Hi jvarkit team,

I am running MantaMerger for merging genome-wide structural variants of multiple ~6000 individuals to population-level SVs. However, it has been running since about three days ago. Is it a reasonable merging time? Besides, is it possible to utilize multiple CPUs to speed it up? Thank you very much.

Best regards, zjgbz

lindenb commented 3 years ago

I agree my tool is quite poor and is just too slow. I strongly suggest you use CNVNator https://github.com/abyzovlab/CNVnator

zjgbz commented 3 years ago

Hi @lindenb ,

No no, it is not poor at all. Your tool is the only merging tool we found for Manta at least for me. We are just wondering if 3-day running means we did anything wrong or else. Since you suggest CNVNator, I checked that, but do you mean that CNVNator also has merging tool for merging SVs from multiple samples? Because now I did not find such function, but if you have used that before, I should go deeper into CNVNator. Thank you very much!

Best regards, zjgbz