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Hardy-Weinberg Equlibrium Testing Using Bcftools

This might be a simple question.Does bcftools by default test for Hardy Weinberg equilibrium?If so,is there any option to take out this testing? I see in the bcftools options the following

-c  Call variants using Bayesian inference. This option automatically invokes option -e.
-e Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equlibrium and testing associations with LRT.

However,I remember there was a separate option '-H' to test for hardy weinberg equilibirum.Can someone make it more clear?

variant bcftools
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written by Kssr Kssr

Out of curiosity why are you trying to use Hardy Weinberg?

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written by Zev.Kronenberg Zev.Kronenberg

I have inbreeding in my samples and have low coverage.My question is does bcftools by default assume HWE and perform the testing ?

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written by Kssr Kssr

I am pretty sure the answer is no, but I am not 100 percent sure. Are you calling all the individuals separately? If so I think you should be fine.

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written by Zev.Kronenberg Zev.Kronenberg

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