From 3cfb6279190a649c6d6c75c67ff3ed5313c1dc13 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 14 Feb 2025 16:11:52 -0800
Subject: [PATCH] Compute kinship using both KING and plink's implementation of
 KING

---
 .../sequenceanalysis/run/variant/KingInferenceStep.java       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
index 4e1e5245f..810e9c76a 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
@@ -139,7 +139,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs1.add("--out");
         plinkArgs1.add(plinkOut.getPath());
 
-        plink.execute(plinkArgs);
+        plink.execute(plinkArgs1);
 
         File plinkOutBed = new File(plinkOut.getPath() + ".bed");
         if (!plinkOutBed.exists())
@@ -154,7 +154,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs2.add("--out");
         plinkArgs2.add(plinkOutKing.getPath());
 
-        plink.execute(plinkArgs1);
+        plink.execute(plinkArgs2);
 
         File plinkOutKingFile = new File(plinkOut.getPath() + ".kin0");
         if (!plinkOutKingFile.exists())