Giters

fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

SURVIVOR convertAssemblytics, issue for "Min size to keep"

Jhuang90 opened this issue · comments

commented

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

commented

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

commented

Hi Dr. Sedlazeck,

Thanks, it makes sense.

Best,
Jun