DeepSomatic

Classify somatic/germline mutations by deep neural networks

Installation

1. Download and install julia v0.5
2. Install Keras with TensorFlow by their guide
3. Install HDF5, StatsBase, PyCall and Libz in Julia

predict

$ julia predict.jl predict ../model/model2.h5 input.bam input.txt > output.txt

By default it accept the txt file generated by AnnoVar.

train new models

First, run julia collect_data.jl cfDNA.bam gDNA.mpileup out.image out.txt for each sample to get a list of.image and .txt files, then call julia data_stat.jl clean to filter them, the result will be put on clean folder. After that, you can run julia ../model1.jl on the clean folder to train the corresponding model.