Pipeline for scoring variants for disruption to genome folding using Akita (Fudenberg et. al. 2020).

Install Akita and its dependencies:
https://github.com/calico/basenji/tree/master/manuscripts/akita

Packages needed:
- Numpy
- Pandas
- Scipy
- Tensorflow
- Basenji and its dependencies
- Cooltools
- Pysam
- Math
- Collection
- Bioseq

Test run on a vcf of structural variants:

python score_var.py --in test/input/subset.somaticSV.vcf --shift_by -1 0 1 --file subset_SV --dir test/output