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Unified Genotyper settings for 200 half-sibs


I've effectively got a sample of 200 individuals, that share one father but each have a different mother. I'm wondering how to best change the default parameters of Unified Genotyper to call variants without bias caused by assumptions of the algorithm.



Best Answer


  • tommycarstensentommycarstensen United KingdomMember

    @Blue I also work with related samples. I would be very interested in hearing about your findings in this thread, when you get further with your analysis. I would be very interested in knowing about the proportion of your variants that have InbreedingCoefficient as a culprit after VQSR. Good luck. Have fun.

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