This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Conduct Hardy-Weinberg Equilibrium Test On Imputed (Mach) Snp Data?

Any advice for conducting Hardy-Weinberg equilibrium test on imputed (MACH) SNP data? My analysis tool (Probabel) doesn't provide this function, and as far as I can tell, neither does Plink.

imputation snp genomics
• 6,844 views • link
updated by zx8754 zx8754 • written by Occam Occam

2 answers

PLINK does HWE test, check for the --hwe option.

• 0 views • link
written by Wen.Huang Wen.Huang

Is it possible he means doing this on dosage data? I find that --hwe does not work if dosage format is specified. For example: 

plink --dosage dosage.dat format=1 --fam dosage.fam --map dosage.map --hardy

or

plink --dosage dosage.dat format=1 --fam dosage.fam --map dosage.map --hwe 0.00001

Neither of these seem to work for me.

• 79 views • link
written by Ryan D Ryan D

As Ryan D mentioned --hwe option on plink doesn't work on dosage data. As far as I know plink can only do association tests with covars and stratas on dosage data. It doesn't support LD calculations either.

To get HWE for dosage data see Approximate and exact tests of Hardy-Weinberg equilibrium using uncertain genotypes.

• 46 views • link
written by zx8754 zx8754

Log in to answer this question.

More posts like this