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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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how to merge SyRI vcfs #256

Closed ChuanzhengWei closed 3 months ago

ChuanzhengWei commented 3 months ago

Hi， SyRI is a very useful tool. I recently used SyRI to obtain about 60 VCF files. I attempted to forcibly merge them using the bcftools merge command but failed because bcftools does not support VCF version 4.3. Although I can change the VCF file version, I am also unsure whether bcftools is suitable for merging SyRI outputs. For merging outputs from SyRI, what method would you recommend? Would you suggest isolating different variant types before merging?

I look forward to your reply！ thank you.

mnshgl0110 commented 3 months ago

Hi @ChuanzhengWei, indeed merging VCFs with complex structural rearrangements as identified by syri is not easy and I am unaware of a method that does that efficiently and correctly. You can fetch SNPs/Indels and then try merging those using bcftools. For larger variants, you can consider fetching them and use some heuristics to merge them. Unfortunately, this will require some scripting.

ChuanzhengWei commented 3 months ago

Thanks for your reply, I think I know how to do it.