Picard - SortSam

[kushakov]

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

"$@"

source /broad/software/scripts/useuse

reuse -q Picard-Tools

"$@"

java -Xmx4g -jar ~/picard-2.12.2/picard.jar SortSam \

INPUT=FILE1.sam, FILE2.bam \

OUTPUT=FILE1.bam, FILE2.bam \

SORT_ORDER=queryname

[Barbara Hill]

Hello,

It looks like you are using Picard from the command line, and not from within GenePattern.

I would suggest contacting the Picard team for help with this question. https://gatkforums.broadinstitute.org/gatk/categories/ask-the-team

If you want to do this with our GenePattern Picard.SortSam module, click the "Batch" checkbox to the right of the input file field and you will be able to submit multiple files.

 https://genepattern.broadinstitute.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00245:4

Please let us know if we can be of further assistance.

Best

Barbara

[kushakov]

Thank you, Barbara

I will reach out for them through GATK.

Best,

Kathy