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downsampling coverage in UnifiedGenotyper

As I saw from this link :http://gatkforums.broadinstitute.org/discussion/1237/how-unified-genotyper-works-retired
downsampling selects some subset reads randomly in Unified Genotype, meanwhile random seed values are affected by several things like multithreading and intervals run in the thread.
I want to ask if there is a "tool" in GATK could select subset reads not randomly, I mean with some intentions.

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