diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 3f966734c43a8167e37052329d5b7ad3d8a412d5..dfd93ff511ac2c64792722893fbb507f8cc6f61e 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -111,7 +111,7 @@ object VcfFilter extends ToolCommand {
           
       if (record.getAttributeAsInt("DP", -1) >= commandArgs.minTotalDepth && 
           genotypes.count(_ == true) >= commandArgs.minSamplesPass &&
-          bamADvalues.count(_ == true) >= commandArgs.minSamplesPass)
+          (commandArgs.minBamAlternateDepth <= 0 || bamADvalues.count(_ == true) >= commandArgs.minSamplesPass))
         writer.add(record)
     }
     reader.close