Understanding TiTvRatioStandard in TiTvVariantEvaluator

shwetaramdasshwetaramdas MIPosts: 3Member

Hi,

I have genotype calls on an exome sequencing dataset, and have used the GATK TiTvVariantEvaluator tool to estimate TiTv ratios for my samples. I'm however having trouble understanding the "TiTvRatioStandard" column, and how I interpret it. My TiTv ratios for known variants are 2.56, below the generally accepted cutoff of 2.8. The TiTv ratios I get for novel variants is also very low (~1.25), which should bring up a red flag, but the values in the "TiTvRatioStandard" column for novel variants is 1.04, and for known variants is 2.56.

I haven't been able to understand what these values mean, and whether I should use them as threshold/quality measures. If someone could point me to more information on this, it would be very helpful.

Thanks,

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  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,196Administrator, GATK Developer admin

    Hi there,

    The "TiTvRatioStandard" metric is the transition to transversion ratio for comp sites; those are the values obtained for the callset you are using as a standard or reference. It seems the values you get for your callset are pretty close to the standard you are using, which is generally a good thing (assuming your standard is of good quality).

    Geraldine Van der Auwera, PhD

  • shwetaramdasshwetaramdas MIPosts: 3Member

    Thanks very much, Geraldine! That helps a lot. My reference dataset (standard) was dbSNP. However, how would I have a TiTvRatioStandard for novel variants? Shouldn't metrics for such variants be unavailable for these?

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