TagPcrSummary: flip default to exclude SA tag when parsing, unless sp…

…ecified
BimberLab · Nov 7, 2020 · ce87a07 · ce87a07
1 parent f5c5c64
commit ce87a07
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/main/java/com/github/discvrseq/tools/TagPcrSummary.java b/src/main/java/com/github/discvrseq/tools/TagPcrSummary.java
@@ -115,7 +115,7 @@ public class TagPcrSummary extends GATKTool {
     public String insertType = null;
 
     @Argument(doc="If provided, this tool will inspect reads for supplemental alignments (SA tag) and parse these as well", fullName = "include-sa", shortName = "sa", optional = true)
-    public boolean includeSupplementalAlignments = true;
+    public boolean includeSupplementalAlignments = false;
 
     @Override
     public boolean requiresReference() {