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Picard - SortSam


I'm using Picard's SortSam tool and was wandering if I can use the same script for 2 files? Meaning, can I do something like that (script below)? What would be the separator sign? Or I would have to run it independently for each file?

Thank you!

source /broad/software/scripts/useuse
reuse -q Java-1.8
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source /broad/software/scripts/useuse
reuse -q Picard-Tools
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java -Xmx4g -jar ~/picard-2.12.2/picard.jar SortSam \
INPUT=FILE1.sam, FILE2.bam \
OUTPUT=FILE1.bam, FILE2.bam \

Best Answer


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