From f2953da357f98abd3c7c88c662446fe498e28f71 Mon Sep 17 00:00:00 2001
From: seppinho <sebastian.schoenherr@i-med.ac.at>
Date: Sun, 3 Mar 2024 13:13:51 +0100
Subject: [PATCH] Write coverage to VCF

---
 src/main/java/genepi/mut/util/MutationServerReader.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/genepi/mut/util/MutationServerReader.java b/src/main/java/genepi/mut/util/MutationServerReader.java
index 4f1bf1b..b5dc1d5 100644
--- a/src/main/java/genepi/mut/util/MutationServerReader.java
+++ b/src/main/java/genepi/mut/util/MutationServerReader.java
@@ -94,6 +94,7 @@ public HashMap<String, Sample> parse(double requiredHetLevel) {
 			variant.setMajorLevel(majorLevel);
 			variant.setMinorLevel(minorLevel);
 			variant.setMeanBaseQualiy(meanBaseQuality);
+			variant.setCoverage(coverage);
 			variant.setType(type);
 
 			sample.addVariant(variant);