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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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SV classification #3627

Open minglibio opened 2 years ago

minglibio commented 2 years ago

Hi all,

I would like to know if anyone has ideas on how should I get the SV types (INS/DEL/INV) from the output vcf of minigraph>cactus>vg-giraffe>vg-call pipeline. Are there any tools I can use? Or should I classify them by myself? If so, what criteria should I use, especially for inversion?

Best, Ming

Chaima-Bouchenak commented 2 years ago

Hello, did you try to manipulate your final VCF file with the vcf/bcf tools package ? it provides many commands for file exploration , hope this link would be helpful.

minglibio commented 2 years ago

Hi @Chaima-Bouchenak Thanks for your suggestion. But I don't find the command of vcf/bcftools that can classify the SVs.

Lucio-Yang commented 1 year ago

Hi, Did you solve the problem, I also encountered the same problem. Can you give me some advice? Thanks!