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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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the parameter of --dup_to_ins #29

Closed Gongjiao94 closed 2 years ago

Gongjiao94 commented 2 years ago

Hi I want to use Jamine to merge SVs generated by cuteSV from multiple individuals. Could you please give me some parameter suggestions for SV calls from cuteSV? In addition, ​I notice that the parameter of "--dup_to_ins" is used in the demo dataset (HG002), so I would like to know when should this parameter be used?

Thanks in advance Jiao

mkirsche commented 2 years ago

Hi,

Sorry for the late reply! The default settings should apply well to cuteSV variant calls. The --dup_to_ins parameter is helpful in cases where the SV caller has a difficult time distinguishing between insertions and duplications (for example when the inserted sequence is somewhat similar but not identical to the surrounding sequence). It converts all small-scale duplications to insertions for the purpose of comparing between callsets, and then converts them back after merging. Another advantage of the parameter is if you are using Iris for SV refinement it is able to polish these calls' breakpoints and sequences when they are temporarily treated as insertions.

I hope that helps! Melanie