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Vcfdist reports excessive FPs #50

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rlorigro opened this issue Sep 20, 2024 · 0 comments
Open

Vcfdist reports excessive FPs #50

rlorigro opened this issue Sep 20, 2024 · 0 comments

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@rlorigro
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3 of 5 of these variants are marked as FPs by Vcfdist (red boxes), despite being approximately correct on the scale of the full tandem haplotype.

Two contributing factors:

  • We cant reasonably expect to evaluate a >50bp VCF with an exhaustive truth VCF containing all SNPs and Indels
  • Vcfdist doesn't appear to be comparing the full haplotype sequences during FP/FN classification, even with the --realign-etc args

We currently get a score of 66% Precision when evaluating the 50bp VCF.
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@rlorigro