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Old 06-21-2011, 09:24 PM   #3
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Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279

If you are looking for one to cut and paste there is one on my introduction thread that will take samples from fastq files straight to sorted bams with dupsmarked. It doesn't do a check for errors after each step, but others could likely suggest a simple method to capture if the exit status of the previous step. Generally, I've not had many issue with errors except when I messed up...
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