11_halibut_deduplicate

## Load software modules
module load picard/2.20.6

## Remove duplicate reads
cd scratch/Halibut_trim_demultiplex/
ls *.sorted.bam | sed 's/.sorted.bam$//' | parallel 'java -Xmx3700m -jar $EBROOTPICARD/picard.jar MarkDuplicates I={}.sorted.bam O={}.deDup.bam M={}_deDupMetrics.txt REMOVE_DUPLICATES=true'