Le Qi
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Recent activity by Le Qi Sort by recent activity-
Hi Gökalp Çelik, I'm trying to produce gVCF files using the wdl pipeline suggested here https://github.com/broadinstitute/gatk/tree/master/scripts/mitochondria_m2_wdl There is no problem producing...
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Hi Gökalp Çelik Thanks for the reply. I understand this is how CollectReadCounts works, so it's intended behavior then. The only reason I called it coverage was that it's the first step to generate...
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Thank you Gökalp Çelik!
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Hi Ricky Magner Thanks for your reply! I was specifically talking about the genotypeGVCFs tool from GATK. I could run the DRAGEN-GATK output gVCF through genotypeGVCFs without problems. I'm curious...
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Hi Gökalp Çelik The workflow works fine on Terra and on my own MacOS with docker, which is not allowed on our HPC. I think the problem is with singularity somehow. I managed to get around the probl...
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Hi Gökalp Çelik I managed to activate gatk conda environment and set THEANO_FLAGS environmental variable, but import gcnvkernel still showed the same error. I've successfully adopted the previous 2...
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Hi Gökalp Çelik I tried the new environmental variable. I have the same errors and I can see the cache files generated in the specified path when I just try to import gcnvkernel. I had similar cach...
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Hi Gökalp Çelik Thanks for your suggestions. I've tried to import gcnvkernel after running this version of gatk docker and it still shows the same error. Maybe I'm missing something else and I'm ru...