fix on no known sites warning

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -51,7 +51,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
     else if (!outputDir.endsWith("/")) outputDir += "/"
 
     val baseRecalibrator = new BaseRecalibrator(this)
-    if (useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
+    if (preProcesBams && useBaseRecalibration && baseRecalibrator.knownSites.isEmpty) {
       logger.warn("No Known site found, skipping base recalibration")
       useBaseRecalibration = false
     }