HaplotypeCaller and low-VAF variants

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vctrymao

• January 20, 2021 20:09

I am using HaplotypeCaller to generate germline variants. I noticed that HaplotypeCaller calls some variants with very low VAF values (see below): 

What is the reasoning behind this? In what situations would this be valid? 

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  Genevieve Brandt (she/her)

  • January 20, 2021 21:29

  Hi vctrymao, are your reporting an abnormal result? Please contain all the information listed in this post so that we can look into the issue.

  You can also check out our troubleshooting documentation for more information about HaplotypeCaller results.

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  vctrymao

  • January 20, 2021 21:48

  No, I'm just wondering how this might happen realistically. 

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  Genevieve Brandt (she/her)

  • January 21, 2021 20:34

  I see, please check out our existing documentation about HaplotypeCaller for more information. If other users have any insight on this, please chime in here!

  Our support policy.

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