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How to run Queue end-to-end starting from FASTQ files
Queue purports to offer users a seamless pipelined integration of BWA, Picard and GATK. Yet Queue requires BAM files as input, implying I would need to call BWA separately to do alignment and then Picard or samtools to convert to BAM, then go back to Queue to work with the BAMs. At this point I run into compatibility issues for instance as described here. So is there a way I can set Queue to take FASTQ files as input?