Classify somatic/germline mutations by deep neural networks
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collect_data.py
model1.py
model2.py
predict.py
readme.md

readme.md

DeepSomatic

Classify somatic/germline mutations by deep neural networks.

There is also a version for Julia.

Installation

  1. Python 3.5+
  2. Keras with TensorFlow by their guide
  3. pip install pysam

predict

$ python predict.py ../model/model2.h5 input.bam input.txt > output.txt

By default it accept the txt file generated by AnnoVar.

train new models

  1. run python collect_data.py cfDNA.bam gDNA.mpileup out.image out.txt for each sample to get a list of .image and .txt files.
  2. run python model1.py to train the corresponding model.