Question: Conduct Hardy-Weinberg Equilibrium Test On Imputed (Mach) Snp Data?
1
gravatar for Occam
8.4 years ago by
Occam390
United States
Occam390 wrote:

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 • 4.6k views
ADD COMMENTlink modified 7.6 years ago by zx87549.7k • written 8.4 years ago by Occam390
3
gravatar for Wen.Huang
8.4 years ago by
Wen.Huang1.2k
Wen.Huang1.2k wrote:

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

ADD COMMENTlink written 8.4 years ago by Wen.Huang1.2k
1

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.

ADD REPLYlink modified 7.6 years ago • written 7.6 years ago by Ryan D3.3k
1
gravatar for zx8754
7.6 years ago by
zx87549.7k
London
zx87549.7k wrote:

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.

ADD COMMENTlink modified 7.6 years ago • written 7.6 years ago by zx87549.7k
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