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# How is the HW proportion test calculated (chi-squared, exact, etc.)?

Member ✭✭
edited October 2012

How is the HW-proportion goodness-of-fit test calculated? Is the GATK using a chi-square (corrected or not) or an exact method? Is the calculation correctly taking into account multiple alleles (where applicable)?

Post edited by Geraldine_VdAuwera on
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## Best Answers

• Broad Institute ✭✭✭✭
Accepted Answer

The code calculates an exact two-sided hardy-weinberg p-value.

• Broad Institute ✭✭✭✭
Accepted Answer

Probability.
The HW code is not written in the GATK directly, but you can access it through Tribble:
http://gatkforums.broadinstitute.org/discussion/1349/tribble

## Answers

• Cambridge, MAMember, Administrator, Broadie admin

Have a look at the genotyper documentation:

http://gatkforums.broadinstitute.org/discussion/1237/using-the-unified-genotyper

That article contains a link to the EXACT mathematical model and to slides covering multiallelic calls.

• Member ✭✭

I have looked through the documentation provided. My interest is in how the VCF annotation tag 'HW' is being calculated, which is not documented in any of the material above (nor on the following page: http://gatkforums.broadinstitute.org/discussion/1268/how-should-i-interpret-vcf-files-produced-by-the-gatk). After looking through a few articles online, it becomes apparent to me that there are different ways of carrying out the test for Hardy-Weinberg proportions that result in different accuracies for estimating the P-values for departures from HW equilibrium.

• Broad InstituteMember, Broadie, Dev ✭✭✭✭
Accepted Answer

The code calculates an exact two-sided hardy-weinberg p-value.

• Member ✭✭

Awesome, thank you. Is the P-value estimated using a probability or likelihood-ratio test statistic?

• Broad InstituteMember, Broadie, Dev ✭✭✭✭
Accepted Answer

Probability.
The HW code is not written in the GATK directly, but you can access it through Tribble:
http://gatkforums.broadinstitute.org/discussion/1349/tribble

• Member ✭✭

Thank you, you have been very helpful :-)

• Member ✭✭

One last question, are the values of the 'HW' tag in percent or phred-scaled?

• Broad InstituteMember, Broadie, Dev ✭✭✭✭

That's in the docs (see the VCF header).

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