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How to classify SV from a graph constructed directly from aligned de novo assemblies #4476

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dudududu12138 opened this issue Dec 10, 2024 · 0 comments

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@dudududu12138
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dudududu12138 commented Dec 10, 2024

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!
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