How to classify SV from a graph constructed directly from aligned de novo assemblies

Open dudududu12138 opened this issue 1 year ago • 1 comments

Hi, I have a graph that constructed directly from aligned de novo assemblies. I used it as a reference and aligned short reads to this graph with vg giraffe. Then I got structural variants with vg pack and vg call and I got the final .vcf result. How can I classify the SV? I mean, how to define insertion,deletion,inversion,duplication? Below is the screenshot of my result. I think I can only trace the evidence by AT in the INFO column.But I don't know how to do it. Do you have any good idea? Thank you so much! 1733835685065

Dec 10 '24 12:12 dudududu12138

Hi. Any updates on this issue? It would be very helpful have this information. Many thanks

Mar 26 '25 15:03 lurens