KING should run --kinship

bbimber · bbimber · commit a5a8863a3d94 · 2025-02-13T10:09:29.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
@@ -184,7 +184,8 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             kingArgs.add(threads.toString());
         }
 
-        kingArgs.add("--related");
+        kingArgs.add("--kinship");
+        kingArgs.add("--rplot");
 
         File kinshipOutput = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(inputVCF.getName()) + ".kin");
         wrapper.execute(kingArgs);

Original file line number	Diff line number	Diff line change
`@@ -184,7 +184,8 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno`
`184`	`184`	`kingArgs.add(threads.toString());`
`185`	`185`	`}`
`186`	`186`
`187`		`- kingArgs.add("--related");`
	`187`	`+ kingArgs.add("--kinship");`
	`188`	`+ kingArgs.add("--rplot");`
`188`	`189`
`189`	`190`	`File kinshipOutput = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(inputVCF.getName()) + ".kin");`
`190`	`191`	`wrapper.execute(kingArgs);`