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max-l/snpSift

Created February 4, 2015 19:01
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snpSift
export HOME_DIR="/home/adminphen/tools/snpEff"
export DB="/home/adminphen/tools/dbsnp137.hg19.vcf"
export JVM_ARGS="-Djava.io.tmpdir=/tmp -XX:ParallelGCThreads=2 -Xmx8G"
cd $HOME_DIR
java $JVM_ARGS -jar $HOME_DIR/SnpSift.jar \
annotate $DB $1 \
> "$1.step1"
java $JVM_ARGS -jar $HOME_DIR/snpEff.jar \
eff -c $HOME_DIR/snpEff.config -o vcf -i vcf -csvStats -stats ? ? \
> "$1.step2"
java $JVM_ARGS -jar $HOME_DIR/SnpSift.jar \
dbnsfp -v ? ? \
> "$1.step3"
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