If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

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
"[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 \

Best Answer


Sign In or Register to comment.