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eblerjana / pangenie

Pangenome-based genome inference
MIT License
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Genotyping with breakpoint deviations #44

Open biozzq opened 1 year ago

biozzq commented 1 year ago

Hi Jana,

Since PanGenie relies on exact kmer matches, I want to know if it will perform well with input SVs that have imprecise breakpoints? Have you investigated how inaccurate breakpoints impact the genotyping results? Thank you.

Best regards, Zheng zhuqing

eblerjana commented 1 year ago

Hi Zheng zhuqing,

I have never really evaluated this, but as you mentioned, since PanGenie uses exact kmer matches, inaccurate breakpoints might be a problem in some cases. We have observed in the past that the variant merging and resulting inaccurate allele sequences seemed to have negative effects on the genotyping accuracy, so my expectation is that it's probably similar with inaccurate breakpoints.

Best, Jana