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HaplotypeCaller on 2000 samples, feasible?
I have previously tested HaplotypeCaller (GATK 2.7) on 100 samples. It takes a long time to run compared to UnifiedGenotyper. Is it feasible to use HaplotypeCaller on 2000 samples? Can I make it run faster other than by using multi-threading? Would it be an advantage for me to run ReduceReads prior to variant calling? I know the details are sparse, but I currently do not have any additional information. Thank you.