From eb84f1d8464d93c1052dcfb9762cb2ac180777b9 Mon Sep 17 00:00:00 2001
From: Ilya Soifer <ilya.soifer@ultimagen.com>
Date: Sun, 20 Nov 2022 23:02:25 +0200
Subject: [PATCH] flow assembly-collapse-hmer-size -> 20

---
 .../haplotypecaller/HaplotypeCallerArgumentCollection.java      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
index 224e3c640dc..ca09a661a61 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
@@ -264,7 +264,7 @@ public enum FlowMode {
                 MIN_BASE_QUALITY_SCORE_SHORT_NAME, "0",
                 FILTER_ALLELES, "true",
                 FILTER_ALLELES_SOR_THRESHOLD, "3",
-                FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, "12",
+                FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, "20",
                 OVERRIDE_FRAGMENT_SOFTCLIP_CHECK_LONG_NAME, "true",
                 FlowBasedAlignmentArgumentCollection.FLOW_LIKELIHOOD_PARALLEL_THREADS_LONG_NAME, "2",
                 FlowBasedAlignmentArgumentCollection.FLOW_LIKELIHOOD_OPTIMIZED_COMP_LONG_NAME, "true",