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Calibration of QUAL field emitted by the Unified Genotyper


I am looking at the distribution of quality scores (QUAL column of VCF) emitted by the Unified Genotyper v1.4 (old version, sorry :)) for SNPs called on 769 samples with 12x coverage HiSeq data. The median quality score is at ~Q750 and the mean at ~Q28000. I was just wondering if you could comment on how well calibrated these quality scores are and whether/how the number of samples and/or coverage would affect them?

Thanks in advance,

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Laurent,

    I'm not quite sure what you mean by calibration for the variant quals? The QUAL will indeed depend on coverage and number of samples, since both can increase or decrease confidence in a given call according to the calling model. Basically it is a question of how many observations are available from which to make a call. If you want to known exactly what is the mathematical relationship you'll need to look at the code of the model calculations for the version that you are using.

  • LaurentLaurent Member, Broadie

    Hi Geraldine,

    Thanks for your answer. What I mean is that QUAL is expressed as a phred score (if I'm not mistaking) and so Q28000 is a rather astronomical number then. I'm just trying to get a sense of how to interpret these values and whether I should really look at them in a relative way (i.e. in the same calling experiment, a site with higher quality has a higher posterior) or if they can be interpreted in an absolute way too.


  • LaurentLaurent Member, Broadie

    Thanks Geraldine,

    This was helpful in clarifying my issue!


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