GATK Queue and the Data Processing Pipeline Posted in Ask the
team | Last updated on  Comments (3)  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?  Return to top Comment on this article in
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