Variant Recalibration on related Samples

Hi GATK team,

our lab has a never ending discussion about running VQSR on related samples or having to exclude them. And i guess we need your help to settle this.

We have a multisample call (UG) run on ~1.500 samples, which contains all sorts of unrelated samples, trios and small families. Our statistician tries to convince us to exclude all related samples, because this might skew the VQSR model. The biologists don't follow this argument, but we are unable to convince each other.
Do related samples disturb the VQSR?

Even more specific - if we run VQSR on tumor/normal pairs - should we expect surprising behaviour of the model or can we just run the recalibration without worries?

thanks for your help in advance,
Oliver

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