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False/True positives in VQSR

SystemSystem Administrator admin
This discussion was created from comments split from: New to the forum? Ask your questions here!.

Comments

  • haopenghaopeng ChineseMember
    Hi, GATK team,
    I'm new to forum and I have a question about VQSR.

    I can't understand why there is false positive in thranches plot. Before scoring sites with VQSLOD, are there false/true positive in new variants already?

    Thanks
  • bshifawbshifaw moonMember, Broadie, Moderator admin

    @haopeng

    Have you already looked at the VQSR documentation for your question? It describes in detail what VQSR does and the plots that it produces.

  • haopenghaopeng ChineseMember
    Thanks for your reply. @bshifaw
    I have read the documentation and I still wonder how you label true and false positive. VQSLOD is log odds of ture probability and false probability. And before scoring the new variants have been labeled true and false positive. So is it using the true/false probability to determine whether a site is true/false positive?
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