Set min coverage to 30 for homoplasmies

seppinho · Dec 23, 2018 · c2e5860 · c2e5860
1 parent 99e0a6a
commit c2e5860
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/main/java/genepi/mut/util/VariantCaller.java b/src/main/java/genepi/mut/util/VariantCaller.java
@@ -41,7 +41,7 @@ public static VariantResult determineVariants(VariantLine line) {
 
 		if (line.getTopBaseFWD() == line.getTopBaseREV() && line.getTopBaseFWD() != '-') {
 
-			if (line.getTopBaseFWD() != line.getRef() && ((line.getCovFWD() + line.getCovREV() / 2) >= 50)) {
+			if (line.getTopBaseFWD() != line.getRef() && ((line.getCovFWD() + line.getCovREV() / 2) >= 30)) {
 
 				if (line.getTopBaseFWD() == 'D') {
 					type = DELETION;