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google / deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
BSD 3-Clause "New" or "Revised" License
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deepvariant as a python package #344

Closed JakeHagen closed 4 years ago

JakeHagen commented 4 years ago

Hi, I am trying to borrow some of the code from deepvariants, specifically importing realigner. What is the best way to do this? Thank you

pichuan commented 4 years ago

Hi @JakeHagen Currently there isn't a very clean way to do this. You can modify the code and build DeepVariant from source: https://github.com/google/deepvariant/blob/r1.0/docs/deepvariant-build-test.md

I'm personally interested in learning more about what you're trying to do - what is the expected input and output. If there's general enough use cases, maybe in the future we can make things easier to import, even though we don't currently have plans for that.

JakeHagen commented 4 years ago

I am doing some work that needs read modification based on variants. These variants come from deepvariant so I was hoping to use the realigner to modify the reads as deepvariant sees them. I often struggle with python imports so I thought I was just missing something. I will look into extracting that code and building. Thank you