Variant Weights Specify how to assign weights to variants. Options are described below. Option Description Equal weights Weights all variants the same. Beta density at MAF Computes the value of the beta distribution density function at the minor allele frequency (MAF) for each SNP using the Alpha value for Beta distribution and Beta value for Beta distribution parameters. Annotation Weight Variable Uses the values given in the variable selected for the Annotation Weight Variable . Important : All weights are squared , so you should enter square roots of weights. Tip : To apply the inverse variance weight , use the Beta distribution with Alpha = 0.5 and Beta = 0.5 . To Choose a Variant Weights Option: Check the Sequence Kernel Association Test (SKAT) box. Click the radio button corresponding to your choice.