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Genotype Concordance after PhaseByTransmission
I'd like to know if someone has tested the concordance from output of PhaseByTransmission with SNP array data.
I have calculated the genotype concordance for the most likely GT combination from the VCF obtained from unified genotyper for a family trio based on the GL values against SNP array data and then did the same for the genotypes obtained after using PhaseByTransmission and I'm seeing a drop in concordance.
Is this to be expected?