I read these two questions on duplicated VCF variants: 1, 2. However, it is not entirely clear to me when duplicated variants can arise (excluding merging artifacts). I want to understand if duplicated variants should be always considered artifacts, or if there are specific use cases where they are needed.
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Do you have a specific problem in mind? There are multiple reasons why duplicate variants may appear (especially when merging datasets), and Stack Exchange doesn't really work well when there are multiple "correct" answers for the same question. – gringer Feb 13 '22 at 22:24
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I don't have a specific problem in mind. I wanted to understand when to expect duplicate variants, since I noticed that some algorithms filter them. Although I understand merging artifacts, I wonder if there are additional corner cases where these duplicate variants appear. The accepted answer can be a community wiki where multiple "correct" answers can be collected, I believe. – gc5 Feb 14 '22 at 17:02
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Okay, probably better asking this question on Reddit r/bioinformatics then. – gringer Feb 14 '22 at 21:28