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Old 12-01-2016, 07:32 AM   #2
PhD Student
Location: Denmark

Join Date: Jul 2012
Posts: 164

Adding 1000 genomes samples might be counterintuitive because you probably already use them as a training set to build the VQSR classifier. There shouldn't be an issue with using hard filtering but regarding sample size for VQSR, you might ask the developers on the GATK forum to get the right answer.
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