Flip alleles for A/T or C/G SNPs with major/minor alleles reversed from reference

Check this box to flip the alleles in the output data set.

Only check this box if:

•	the two alleles for a SNP are either A and T or C and G, and

•	the annotation data set has the complement of the major and minor allele for its major and minor alleles.

Checking this box when the conditions are not met will result in flipped SNPs . Their status will be changed to "Complement of ref".

To Specify This Option:

Click within the check box.