Conduct Hardy-Weinberg Equilibrium Test On Imputed (Mach) Snp Data?

Question

[Occam]

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.

Answer 1

[Wen.Huang]

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

[Ryan D]

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.

Answer 2

[zx8754]

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.