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Picard - SortSam

Hello,

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
"[email protected]"

source /broad/software/scripts/useuse
reuse -q Picard-Tools
"[email protected]"

java -Xmx4g -jar ~/picard-2.12.2/picard.jar SortSam \
INPUT=FILE1.sam, FILE2.bam \
OUTPUT=FILE1.bam, FILE2.bam \
SORT_ORDER=queryname

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