Annotation Analysis Group Variable for Collapsing Rare Variants

The Annotation Group Variable for collapsing Rare Variants) field is used to indicate the annotation variable designating rare variants to collapse together to form a single genotype . Typically, the values in this column are the names of the genes in which the different markers are located.

During the recoding, all markers whose frequency of occurrence is less than the specified MAF threshold and have the same annotation group value are grouped together into one genotype. The grouped rare variants are listed in one column in the output data set and one row in the output annotation data set . Markers whose frequency exceeds the MAF threshold are not included in this group, but rather are considered to be distinct genotypes and are output in separate columns and rows.

To Specify the Annotation Analysis Group Variable:

Select Use Dominant Coding collapsing across rare variants in a group as the Rare Variant Recoding method.

Specify a MAF Threshold for Rare Variants .

Specify the Annotation SAS Data Set .

All of the variables in the specified annotation data set are displayed in the Available Variables field.

Examine the list of available variables.

Highlight the variable that specifies rare allelic variants.

Click to add the highlighted variable to the Annotation Analysis Group Variable field.

Note : The values of other variables in the annotation data set for the first rare variant in each analysis group only are included in the Output Annotation Data Set .