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bacpop / ggCaller

Bifrost graph gene caller.
MIT License
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Frameshift mutations #11

Closed mbhall88 closed 10 months ago

mbhall88 commented 11 months ago

Love this method!

I'm trying to understand what would happen with the annotation/prediction process if a genome in the DBG has a frameshift mutation in a gene. Would that gene not get annotated? And would it mess up downstream annotations?

samhorsfield96 commented 11 months ago

Hi, a frameshift will cause the sequence to be missed by the initial gene identification step. However, Panaroo includes a gene refining step, meaning that if intact homologues of the pseudogene are present in other genomes, the sequence should be found, clustered and functionally annotated, with an additional label of "potential pseudogene".

mbhall88 commented 10 months ago

Ah very cool. Thanks for the explanation.