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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