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Old 09-30-2013, 05:18 AM   #2
harryzs
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Location: Germany

Join Date: Dec 2010
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"GATK accept interval files for processing subsets of the genome in Picard-style interval lists"
http://www.broadinstitute.org/gatk/g...rticle?id=1204

I think you just need to change your bed file to <Picard-style interval> format.
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