Updated M2 parameters to make them consistent with HC (#8186)

* Updated M2 parameters to make them consistent with HC
broadinstitute · Feb 9, 2023 · b7f24ff · b7f24ff
1 parent d3b2c5c
commit b7f24ff
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
@@ -336,8 +336,7 @@ 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",
-                FlowBasedArgumentCollection.FLOW_MATRIX_MODS_LONG_NAME, "10,12,11,12",
+                FLOW_ASSEMBLY_COLLAPSE_HMER_SIZE_LONG_NAME, String.valueOf(AssemblyBasedCallerUtils.DETERMINE_COLLAPSE_THRESHOLD),
                 OVERRIDE_FRAGMENT_SOFTCLIP_CHECK_LONG_NAME, "true",
                 FlowBasedAlignmentArgumentCollection.FLOW_LIKELIHOOD_PARALLEL_THREADS_LONG_NAME, "2",
                 FlowBasedAlignmentArgumentCollection.FLOW_LIKELIHOOD_OPTIMIZED_COMP_LONG_NAME, "true",