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Service note: Geraldine is on vacation this week; other members of GSA will be responding to questions, but they have a lot of work besides this, so be aware that responses may be a little slower than usual. Thank you for your patience.

Genotype Concordance after PhaseByTransmission

VivekVivek Posts: 2Member ✭
in Ask the 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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