Hardy-Weinberg Equlibrium Testing Using Bcftools

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11.5 years ago

Kssr ▴ 110

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 • 4.6k views

ADD COMMENT • link 11.5 years ago by Kssr ▴ 110

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

ADD REPLY • link 11.5 years ago by Zev.Kronenberg 12k

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

ADD REPLY • link 11.5 years ago by Kssr ▴ 110

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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.

ADD REPLY • link 11.5 years ago by Zev.Kronenberg 12k

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