Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Calculation of PL and GQ by HaplotypeCaller and GenotypeGVCFs Follow

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    Roller, Eric

    Can you confirm that this definition of GQ is different than the GQ defined in the VCF spec? From the spec:

    GQ (Integer): Conditional genotype quality, encoded as a phred quality −10log10 p(genotype call is wrong, conditioned on the site’s being variant). 

    It appears the normalization step that is performed would give a different answer than what is defined by the spec.

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