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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR convertAssemblytics, issue for "Min size to keep" #171

Closed Jhuang90 closed 1 year ago

Jhuang90 commented 1 year ago

Hi Dr. Sedlazeck,

I like using SURVIVOR you developed, it is really convenient. I just got a question about 'convertAssemblytics', I found when I converted my Assemblytics outcome (bed file) to a VCF file, I used 10 bp as a filter for "Min size to keep". However, when I checked the VCF outcome, it seems that all SV with exactly 10 bp size got removed from the vcf file, it that common to see? or is something wrong with "Min size to keep" setting? My SURVIVOR version is Version: 1.0.7.

Thanks, Jun

fritzsedlazeck commented 1 year ago

Dear Jun, the min size is > not >= . I think that's what you are seeing here. Cheers Fritz

Jhuang90 commented 1 year ago

Hi Dr. Sedlazeck,

Thanks, it makes sense.

Best, Jun