Ignore half-called GTs

Author: bbimber

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

@@ -227,6 +227,10 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep
             args.add(String.valueOf(maxRam));
         }
 
+        // NOTE: tools like sawfish can report half-called genotypes, like 0/.. For now, be most conservative in PCA:
+        args.add("--vcf-half-call");
+        args.add("missing");
+
         args.addAll(getClientCommandArgs());
 
         getWrapper().execute(args);