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CalculateGenotypePosteriors and excess heterozygotes

tmotmo Duke UniversityMember

In a partially inbreeding species we found an excess of called heterozygotes (a peak of observed/expected heterozygosity = 1.0). Is this because of CalculateGenotypePosteriors? Can we turn this off? Or better yet, can one set a prior for called heterozygosity / expected heterozygosity (an expected distribution of the inbreeding coefficient)?

The histogram of observed/expected heterozygosity is attached (with the low tail truncated).

Thanks!

Best Answer

Answers

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭
    edited May 2015

    Stupid question: How do you know, what your expected heterozygosity is? It could deviate from HWE. How many samples are you dealing with? Is this low coverage data?

  • tmotmo Duke UniversityMember

    We know from previous studies that this species has an inbreeding coefficient around 0.9 (observed/expected heterozygosity = 0.1), so we expect most individuals will be fairly homozygous. This is genotyping by sequencing data with fairly high coverage, although individuals may have light coverage at a particular locus (192 individuals GBSed in 1 lane). However, more conservative filtering would bring its own biases.

    Given this level of inbreeding, we are cautious about inferred heterozygotes, and it is implausible to see many loci with inferred/expected heterozygosity near 1.0. The excess of inferred heterozygotes near Hardy-Weinberg frequency suggests some Hardy-Weinberg expectation in genotype calls, but I have been unable to locate that in the documentation.

    Finally, to correct my original question, CalculateGenotypePosteriors was not used in these analyses.

    Thanks

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