There are three steps in CNVbd. The first step is to use "extractfeatures.Py" to extract the features of BAM files. The second step is to use "prediction.Py" to predict the extracted features. The third step is to use "mybds.Py" to get the final result.
Use config Ini to configure parameters.

The file "ExtractFeatures.Py" uses the parameters under "[extractfeatures]". In the file, "bamfilepath" is the path of BAM file, "chrfile" is the path of the corresponding reference fasta file, the "binlen" is the bin length which is set to be 1500bp by default, and the "dc" is a parameter related to sequencing depth. When the extracted DS features are all 1, please increase the size of this parameter appropriately, and the default is 0.5.

The file "prediction.Py" uses the parameters under "[prediction]". In the file, "predictionfilepath" is the path of the file generated by the feature extraction in the previous step which is the data used for prediction, "binlen" is the bin length of 1500bp by default, and "model" is the model used for prediction.

The file "myBDS.Py" uses the parameters under "[bds]". In the file, "predictionresultfile" is the result of the second step model prediction, "bamfilepath" is the path of BAM file,  "chrfile" is the path of the corresponding reference fasta file, and "binlen" is still the bin length of 1500bp by default.

The final result of CNBbd is a TXT file named "_result_border.txt".