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Hi GATK team,
I have a question about VQSR. For "VariantRecalibrator" I used as annotations: -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff -mode SNP -tranche 100.0 -tranche 99.9 -tranche 99.0 -tranche 90.0; for "ApplyRecalibration" --ts_filter_level 99.0. I have an exome dataset of more than 200 samples but samples belong to at least 15 families. I wonder if I was wrong to use InbreedingCoeff as annotation and how much it could affect the final number of PASS variants.