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Old 10-09-2013, 02:50 AM   #11
choishingwan
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Location: Hong Kong

Join Date: Feb 2012
Posts: 21
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I thought fixMate is no longer required by the GATK pipeline? And if you want to perform the fixMate then sortSam, you can run FixMate with the SO options in SortSam, then your output will be automatically sorted in one go. It is also a good idea to always include Create_Index=TRUE in the pipeline to make sure you have the index for every steps just to be safe
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