diff --git a/src/VariantOutput.java b/src/VariantOutput.java index f364627..c875f68 100644 --- a/src/VariantOutput.java +++ b/src/VariantOutput.java @@ -404,7 +404,7 @@ void updateOutputVariant(int sample, VcfEntry entry, int groupNumber) throws Exc } else if(entry.hasInfoField("SUPP")) { - varCallsCount = Integer.parseInt("SUPP"); + varCallsCount = Integer.parseInt(entry.getInfo("SUPP")); } consensus[groupNumber].setInfo("VARCALLS", varCallsCount + Integer.parseInt(consensus[groupNumber].getInfo("VARCALLS")) + "");