diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
index d7f0961fc4dcaf2dd03f7773a9826908e9d00794..443a50d2ea52460d6a47b0b6619ad55b7560e54a 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/Stats.scala
@@ -165,7 +165,7 @@ case class Stats(generalStats: mutable.Map[String, mutable.Map[Any, Int]] = muta
                      sampleDistributions: List[String],
                      contig: Option[String]): Unit = {
     outputDir.mkdirs()
-    this.writeToFile(new File(outputDir, "stats.json"),
+    this.writeToFile(new File(outputDir, s"${contig.getOrElse("total")}.json"),
                      samples,
                      genotypeFields,
                      infoFields,
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
index 925f2ac08627b13563414f72bb32b2802041ebfe..3b69160616f1859f0b5d6b37969f47f7a86df997 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
@@ -110,11 +110,11 @@ object VcfStats extends ToolCommand {
 
     val completeStatsJson = regions
       .flatMap(_.map(_.chr))
-      .foldLeft(ConfigUtils.fileToConfigMap(new File(cmdArgs.outputDir, "stats.json"))) {
+      .foldLeft(ConfigUtils.fileToConfigMap(new File(cmdArgs.outputDir, "total.json"))) {
         case (map, contig) =>
           val contigMap = ConfigUtils.fileToConfigMap(
             new File(cmdArgs.outputDir,
-                     "contigs" + File.separator + contig + File.separator + "stats.json"))
+                     "contigs" + File.separator + contig + File.separator + s"$contig.json"))
           ConfigUtils.mergeMaps(map, contigMap)
       }