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Phred and GQ

What is the difference between Phred and GQ(Genotype quality)? Which are the values for a good cut-off?

snp vcf ngs genome next-gen

1 answer

Phred scale is usually used for representing the base error probability in lograrithm format:

$Phred score = -10 log_10 error probability$

genotype quality is how certian the genotype calling algorithm is about the genotype called. It is usually displayed in 10*log(relative_score_of_genotype) format too.

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