Question

Phred and GQ

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6.0 years ago

patrick.mackay • 0

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 • 1.1k views

ADD COMMENT • link updated 6.0 years ago by hoseintoossi ▴ 40 • written 6.0 years ago by patrick.mackay • 0

score 2 · Accepted Answer · 2018-04-10

2

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6.0 years ago

hoseintoossi ▴ 40

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.

ADD COMMENT • link 6.0 years ago by hoseintoossi ▴ 40