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.

Piping to Picard in Windows

Our group is trying to get a bwa-sampe/picard pipeline running on a windows cluster, and we're having problems piping to picard.

On unix, we'd use 'java -jar picard.jar SortSam I=/dev/stdin ...' but windows doesn't recognize /dev/stdin (even under cygwin) and complains that the file doesn't exist.

We can, of course, write the sam file out in its entirety, but we'd rather save the time and writing to disk, if possible.

Anyone have a solution (other than switch to unix)? Thanks in advance.



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