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allgenesconsidered/2_picard.sh

Created November 27, 2017 22:32
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2_picard.sh
#!/bin/bash
PI="/data/home/molvera/opt"
cd /data/home/molvera/wgs-patient-data
for SAMPLE in "MN_P1_S5" "NF_P1_S1" "BT_P1_S2"
do
java -Xmx10g -jar $PI/picard.jar SortSam\
INPUT=./sam/$SAMPLE.sam\
OUTPUT=./bam/$SAMPLE.bam\
SORT_ORDER=coordinate
java -Xmx10g -jar $PI/picard.jar MarkDuplicates\
INPUT=./bam/$SAMPLE.bam\
OUTPUT=./bam/$SAMPLE\_d.bam\
METRICS_FILE=./bam/$SAMPLE\_metrics.txt
java -Xmx10g -jar $PI/picard.jar BuildBamIndex\
INPUT=./bam/$SAMPLE\_d.bam
done
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