From 8743431bb8575b8e226ed9d1205641c10182b9b7 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 6 Feb 2024 16:20:45 -0800
Subject: [PATCH] Fix DeepVariant arg name

---
 .../sequenceanalysis/run/analysis/DeepVariantAnalysis.java      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
index f46ffe802..51c6bf296 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/DeepVariantAnalysis.java
@@ -226,7 +226,7 @@ public void execute(File inputBam, File refFasta, File outputGvcf, PipelineOutpu
             tracker.addIntermediateFile(dockerBashScript);
 
             List<String> bashArgs = new ArrayList<>(Arrays.asList("/opt/deepvariant/bin/run_deepvariant"));
-            bashArgs.add("--normalize_reads=true");
+            bashArgs.add("--make_examples_extra_args='normalize_reads=true'");
             bashArgs.add("--ref=/work/" + refFastaLocal.getName());
             bashArgs.add("--reads=/work/" + inputBamLocal.getName());
             bashArgs.add("--output_gvcf=/work/" + outputGvcf.getName());