07 Remove PCR Duplicates using PICARD

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Neranjan Perera edited this page Dec 5, 2018 · 2 revisions

module load picard/2.9.2
export _JAVA_OPTIONS=-Djava.io.tmpdir=/scratch

cd ../${d3}/

java -jar $PICARD MarkDuplicates \
        INPUT=../${d2}/${INPUT_FILE_NAME}_filtered_sort.bam \
        OUTPUT=${INPUT_FILE_NAME}_nodup.bam \
        REMOVE_DUPLICATES=Ture \
        METRICS_FILE=${INPUT_FILE_NAME}_metrics.txt \
        CREATE_INDEX=True