Update KING arguments for non-standard chromosomes

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java

@@ -90,11 +90,8 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             plinkArgs.add("--chr");
             plinkArgs.add(StringUtils.join(toKeep, ","));
         }
-        else
-        {
-            plinkArgs.add("--allow-extra-chr");
-        }
 
+        plinkArgs.add("--allow-extra-chr");
         plinkArgs.add("--silent");
 
         plinkArgs.add("--max-alleles");