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GATK germlineCNVCaller with GPU and CUDA
Hello I am running GATK germlineCNVCaller on a machine with an Nvidia GPU that seems to be configured correctly as it runs an test program in the GPU. Without the GPU on 16 CPUs it can take 2.5 days to call a CNV on one sample (case mode). I have not been able to get Theano to work with the GPU having tried different versions of Theano, cuda (8, 9 and 10), cudnn etc. One of the error messages suggests that an older version of cudnn is require but I have not been able to get that version to install.
Should I expect the germlineCNVCaller to work with Theano on the GPU or is this something that has not been tested.