MetaRNN for pathogenicity prediction of nsSNVs and nfINDELs

Quick start guide

1. Download file package (file size: 13G):

   wget -c https://usf.box.com/shared/static/c4656df0rz10vw6z7ra11mkw69ulr9d3 -O MetaRNN.tar.gz 
   

   OR open the save link in any web browser: https://usf.box.com/shared/static/c4656df0rz10vw6z7ra11mkw69ulr9d3

   OR get it from figshare.

2. Extract downloaded folder:

   tar -xf MetaRNN.tar.gz
   cd MetaRNN
   

3. Create conda environment with required packages and activate the virtual environment:

   conda env create -f environment.yml
   conda activate MetaRNN
   

4. Run example VCF file in hg38 genome assembly:

   python ./MetaRNN.py hg38 test.vcf
   

Notes

• Supplementary Tables and model analyses associated with the publication are available under folders Data and Notebooks.

• Tensorflow models of MetaRNN and MetaRNN-indel are available under Resources/Models, with names RNN_DNN_adam.h5 and RNN_DNN_indel_adam.h5, respectively.

• The code for the MetaRNN pipeline, including data preparation and making predictions, is available under Resources/Pipeline.