Fix command

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala

@@ -128,8 +128,8 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
       multiArg("-frequentist", frequentist) +
       conditional(fullParameterEstimates, "-full_parameter_estimates") +
       optional("-method", method) +
-      optional("-pheno", pheno)
-    conditional(summaryStatsOnly, "-summary_stats_only") +
+      optional("-pheno", pheno) +
+      conditional(summaryStatsOnly, "-summary_stats_only") +
       conditional(covAll, "-cov_all") +
       conditional(covAllContinuous, "-cov_all_continuous") +
       conditional(covAllDiscrete, "-cov_all_discrete") +