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author | pcingola |
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date | Fri, 20 Apr 2012 11:22:59 -0400 |
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#!/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"