Classify somatic/germline mutations by deep neural networks
- Download and install julia v0.5
- Install Keras with TensorFlow by their guide
- Install HDF5, StatsBase, PyCall and Libz in Julia
$ julia predict.jl predict ../model/model2.h5 input.bam input.txt > output.txt
By default it accept the txt file generated by AnnoVar.
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.