GeneticVariant var2 = genotypeData.getSnpVariantByPos(riskE2.getChr(), riskE2.getPos());
if (var2.getCallRate() < 0.75) {
excludeSNPs[t] = true;
excludeList.add(riskE2.getRsName());
continue;
<BUG>}
try {
Ld ld = var1.calculateLd(var2);
if (ld.getR2() >= rSquare) {</BUG>
excludeSNPs[t] = true;

GeneticVariant var2 = genotypeData.getSnpVariantByPos(riskE2.getChr(), riskE2.getPos());
if (var2.getCallRate() < 0.75) {
excludeSNPs[t] = true;
