UDACHA pipline

This repository contains code used to build a of allele-specific chromatin accessibility sites.

1. The SNP calling step is performed by the https://github.com/autosome-ru/ADASTRA-pipeline using GATK
2. Grouping according to cell types performed by scripts/advanced_badgroups/plink_clustering.sh using plink2
3. Group-specific BAD reconstruction is performed by scripts/advanced_badgroups/make_advanced_badgroups.py using BABACHI
4. ASE calling is performed by scripts/mixalime/make_release.sh using MIXALIME