Conda for GATK4

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manolis

• November 26, 2024 14:50

REQUIRED for all errors and issues:
a) GATK version used: 4.6.1.0
b) Exact command used: python -c "import vqsr_cnn"

Hi, not sure if it is an installation issue from my side, but after conda installation as test I ran "import vqsr_cnn" and I get the below error:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'vqsr_cnn'

With the 4.6.0.0 I do not have any error; just in case ... If I'm correct the CNN was replaced with NVS, could be the issue of the error message with the 4.6.1.0 ?

Thank you

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• 

  Gökalp Çelik

  • December 02, 2024 08:02

  Hi manolis

  CNNScoreVariants tool is deprecated therefore certain python libraries were removed from our conda environment. NVScoreVariants is the new tool that depends on pytorch but not tensorflow. 

  If you wish to use the old tool you have to stick with 4.6.0.0 and prior. 

  Regards. 

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