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I am starting the GATK workflow on several hundred exomes working with fastq.gz files. I am using fastqToSam in Picard to convert my fastq files (paired end) to uBAM. This works fine on one set of files but I have many hundred to process. It looks like --USE_SEQUENTIAL_FASTQS will help me, but I can't find documentation on syntax beyond the fact that it is boolean. Can you tell me how I need to specify files to make this work? Is there any way that I can use a wildcard and provide a directory of fastq files? I'm wondering what a typical workflow is for processing hundreds of samples.


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