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Basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

Variant analysis

basenji_sad.py

Compute SNP Activity Difference (SAD) scores for SNPs in a VCF file.

Arguments Type Description
params_file Text table Model configuration parameters.
model file TensorFlow Saver file Trained Basenji model.
vcf_file VCF Variant Call Format file describing bi-allelic variants.

basenji_sed.py

Compute SNP expression difference (SED) scores for SNPs in a VCF file.

Arguments Type Description
params_file Text table Model configuration parameters.
model file TensorFlow Saver file Trained Basenji model.
genes_hdf5_file HDF5 HDF5 file with gene sequences and descriptions.
vcf_file VCF Variant Call Format file describing bi-allelic variants.

basenji_sat_vcf.py

Perform an in silico saturated mutagenesis of the sequences surrounding SNPS in a VCF file.

Arguments Type Description
params_file Text table Model configuration parameters.
model file TensorFlow Saver file Trained Basenji model.
vcf_file VCF Variant Call Format file describing bi-allelic variants.