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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.