Fix DeepVariant arg name

BimberLab · Feb 7, 2024 · 8743431 · 8743431
1 parent a188380
commit 8743431
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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());