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Genotype Concordance after PhaseByTransmission

VivekVivek Member
edited January 2013 in Ask the GATK team

Hi all,

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?

Thanks!

Post edited by Geraldine_VdAuwera on
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