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FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data

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What is the Objective value in the output

Rashesh7 opened this issue · comments

commented

Hi,
I apologize if this is mentioned somewhere already, but what is the Objective value in the output. And how can it be used to qc the prediction?

Thanks,
Rashesh

commented

The objective value is a regularized count of reads explained by the selected HLA genotype.

QC is though since the objective function is the optimally achievable score. You could enumerate the solutions and create other (sub)-optimal solutions and compare their score and manually check the results in an alignment viewer of your choice.