tp-baseline vs tp-called

[Alexandra Vatsiou]

Hello,

I am using vcfeeval and I can see that most of the times tp-baseline and tp-called are the same number, as documentation describes "the variants in tp.vcf and tp-baseline.vcf are equivalent."

However, I have seen that there are a few cases that the number is slightly different. Why would this be? 

Best,

Alexandra

[Len Trigg]

Equivalence is determined at the haplotype level (so the matches do not need to be one to one).

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[Alexandra Vatsiou]

thanks