Segment and Encode VCF

Edit ./cpp/config_sample to include correct data
Edit Snakefile to include correct paths
snakemake

run plink on a VCF file

plink --vcf /path/to/vcf/ --genome

make input to CNN model

python ./python/scripts/make_CNN_input.py /path/to/sampleIDs /path/to/encoding_file /path/to/plink_IBD_file /path/to/ID_CNN_output /path/to/encoding_CNN_output

run model

python ./python/scripts/main_cnn.py /path/to/sampleIDs /path/to/encoding_file /path/to/ID_CNN /path/to/encoding_CNN