GATK Queue and the Data Processing Pipeline
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What is the best way to get Queue to optimize utilization of a given number of cores in an SGE cluster? The DataProcessingPipeline.scala has a hidden parameter "scatter_gather" which sets the nContigs variable. Is it safe to use this option? For example, if you had 100 cores available in your cluster could you set the option to 100? Is there any advantage to setting it higher?

Without setting it, Queue appears to set the nContigs value based on the number of chromosomes in the BAM input. So if using a whole genome BAM it's 25, your example Chr20 data it's 1, or with an unaligned BAM it's 0. So if starting with unaligned data, it appears to run on a single core?


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