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@daTokenizer

daTokenizer/generate_sention_pon.sh

Created March 7, 2019 12:28
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generate_sention_pon.sh
#! /bin/sh
export SENTIEON_PROJECT_HOME=/home/ubuntu/sentieon
export SENTIEON_LICENSE=$SENTIEON_PROJECT_HOME/emedgene_eval.lic
export SENTIEON_BIN=$SENTIEON_PROJECT_HOME/sentieon-genomics-201808.03/bin/sentieon
export REFERENCE=/opt/data/ref/Human/Hg19/genome_ref/hg19.fa #$SENTION_DATA_DIR/reference/hg19/hg19.fa
export BED_FILE=/opt/data/input/UNIQUE_Agilent_130_5.bed
export NUMBER_THREADS=8
echo -n "started at "; date +%H:%M:%S
$SENTIEON_BIN driver -t $NUMBER_THREADS -r $REFERENCE -i $1 -q $2 -i $3 -q $4 --algo CNV --target $BED_FILE --create_pon pon.hdf5
echo -n "ended at "; date +%H:%M:%S
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