If you want to run Picard's Mark Duplicates on Lonestar, do roughly this:
The output metrics file is required and worth screening before you go further. |
Picard is also installed on fourierseq at /usr/local/genome/bin and the jar files are in fourierseq user's paths. General syntax for using picard jar files: java -Xmx4g -jar /usr/local/genome/bin/jarfilename |
Find picard document here