Question about definition of startOverlap and endOverlap in VAT

I have been using your variant annotation tool VAT and I have a question about what the definition is of startOverlap and endOverlap. I went through the example workflow and I have annotated another file, but I do not have any variants annotated with these types in my files. I went through your website but I could not find a listing of definitions for the terms. Thank you.

These features are annotated only for indels. Essentially, when a indels affects the START of a gene or the end of a gene, it is annotated as startOverlap and end Overlap respectively. You can find extensive documentation for VAT at Please click on "Documentation" tab. Please let me know if you have any more questions.

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