Body: <p>I read these two questions on duplicated VCF variants: <a href="https://bioinformatics.stackexchange.com/q/7105/1771">1</a>, <a href="https://bioinformatics.stackexchange.com/q/7126/1771">2</a>.
  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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-13T22:24:24.433Z
Comments.Text: 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.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-14T17:02:47.550Z
Comments.Text: 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.
Comments.UserDisplayName: gc5
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-14T21:28:17.377Z
Comments.Text: Okay, probably better asking this question on [Reddit r/bioinformatics](https://www.reddit.com/r/bioinformatics/submit) then.
Comments.UserDisplayName: gringer
Tags: <vcf><variant-calling>
Title: When can we have duplicated variants in a VCF file, excluding artifacts?
ThreadText: # When can we have duplicated variants in a VCF file, excluding artifacts?
  
  (Asked by: username_0 on 2022-02-11)
  
  I read these two questions on duplicated VCF variants: [1](https://bioinformatics.stackexchange.com/q/7105/1771), [2](https://bioinformatics.stackexchange.com/q/7126/1771).
  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.
  
  **Tags:** vcf, variant-calling
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_0**: 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.  
  > **username_1**: Okay, probably better asking this question on [Reddit r/bioinformatics](https://www.reddit.com/r/bioinformatics/submit) then.  
  
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  ## 0 answers
  
  