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arq5x committed Mar 19, 2015
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Expand Up @@ -33,7 +33,7 @@ A workflow for the above steps is given below.
# decompose, normalize and annotate VCF with snpEff.
# NOTE: can also swap snpEff with VEP
zless $VCF \
| sed -i 's/ID=AD,Number=./ID=AD,Number=R/' $VCF
| sed 's/ID=AD,Number=./ID=AD,Number=R/'
| vt decompose -s - \
| vt normalize -r $REF - \
| java -Xmx4G -jar $SNPEFFJAR -formatEff GRCh37.75 \
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