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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
354 stars 47 forks source link

vcftobed info #53

Closed yuntwang closed 5 years ago

yuntwang commented 5 years ago

Hi, recent I use the sub command vcftobed convert my vcf to bedpe and a little question: my bedpe like this: chr11 5200306 5200306 chr11 5208306 5208306 DUP0090SUR , - + DUP chr11 5200309 5200309 chr11 5200348 5200348 INV0088SUR , - - INV and I know the first 3 columns are the first breakpoint and the 4-6 columns are the stop breakpoint. and the 7 column are SV type, and the 8-10 means? the 9 means the first breakpoint dna strand info,10 means the stop breakpoint dna strand info?

fritzsedlazeck commented 5 years ago

Hi, I tried to stick to the output that Lumpy provided. The , is just a space holder. - and + are indicating the directions parsed. That can be used for how to validate these SV later. 10 is actually the SV type. 7 is the ID from the vcf file that you used as the input.

Does that help? Thanks for reaching out. Fritz

yuntwang commented 5 years ago

Thanks