If the vcf file that syri output can support to construct VG graph genome?

schneebergerlab / syri

Synteny and Rearrangement Identifier

https://schneebergerlab.github.io/syri/

MIT License

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If the vcf file that syri output can support to construct VG graph genome? #122

Closed BRLIA closed 2 years ago

BRLIA commented 2 years ago

Hi, I'm going to construct graph genome by VG, and I want to use the SVs detected by SyRI, but I don't know if the VCF file that SyRI output can support it. Thanks

mnshgl0110 commented 2 years ago

The output VCF is based on the VCFv4.3 format, so if VG reads that then it should work. However, I am not sure whether VG handles all the different types of genomic differences that SyRI identifies (for ex: translocations or HDRs) . So, you might need to filter it out. This question is probably better suited for the VG developers.

BRLIA commented 2 years ago

OK，I will try it. Thank you for your help