--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_2_1a/snpEff_2_1a/scripts/test.Broad_NS_SYN.sh	Fri Apr 20 11:22:59 2012 -0400
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+REF=GRCh37.66
+
+IN_VCF=$HOME/snpEff/1kg/test.Broad_NS_SYN.vcf.gz
+OUT_VCF=all.vcf
+
+# Run SnpEff
+./scripts/snpEffXL.sh eff -v -noStats -o vcf $REF $IN_VCF > $OUT_VCF
+
+# Calculate number of lines
+SILENT=`cat $OUT_VCF | grep "SILENT" | wc -l`
+MISSENSE=`cat $OUT_VCF | grep "MISSENSE" | wc -l`
+NONSENSE=`cat $OUT_VCF | grep "NONSENSE" | wc -l`
+SILENT_AND_MISSENSE=`cat $OUT_VCF | grep "SILENT" | grep "MISSENSE" | wc -l`
+
+PSILENT=`echo "100 * $SILENT/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l`
+PMISSENSE=`echo "100 * $MISSENSE/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l`
+PNONSENSE=`echo "100 * $NONSENSE/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l`
+
+echo -e "Silent              :\t$SILENT ($PSILENT %)" 
+echo -e "Missense            :\t$MISSENSE ($PMISSENSE %)"
+echo -e "Nonsense            :\t$NONSENSE ($PNONSENSE %)"
+echo -e "Silent and missense :\t$SILENT_AND_MISSENSE"
+