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