avocado-imputation edited scripts for our own usage and ease of implementation with our own data.
the file "avocado.txt" contains step by step instructions to generate all the submittable slurm scripts. it also calls the .py scripts provided in this repository. the .py scripts provided here are those modified slightly from the avocado-imputation .py scripts generated by Jacob Schreiber.
Generally, this pipeline starts by taking bigwigs to generate per chromosome bedgraphs, then converts these to arcsinh numpy arrays per chromosome, which are then integrated into the roadmap model.
This model is then used for imputation of any and all marks input using the last line of code in the "avocado.txt" file.