vcfeval score and decompose

[Alexandra Vatsiou]

Hello, 

I have 2 questions for vcfeval: 

1. vcfeval -score

When I run vcfeval with the --vcf-score-field=STRING option I have in the output something as follows: 

#score  true_positives_baseline false_positives true_positives_call false_negatives precision   sensitivity f_measure

From which file is the score derived from? baseline or called? 

2. vcfeval - decompose

if -- decompose option is not activated, would vcfeval still account for differences in the vcf file representation e.g. if in baseline a variant is SNV but in called is within a complex variant? 

Thank you.

Best,

Alexandra

[Len Trigg]

Hi Alexandra,

1) The score field comes from the calls file.

2) Yes it definitely can, as long as the matching can be done in terms of whole calls. In your case, if your baseline had the SNV as well as whatever other variants were required to be equivalent to the single called complex variant. What the decompose option buys you is some ability to match smaller parts of long calls, e.g. if part of the single complex call variant matched the baseline SNV but other baseline variants needed to complete the match were missing.

Cheers,

Len.

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