This repository is an implementation(wrapper) for Protein-coding repeat polymorphisms strongly shape diverse human phenotypes paper code's code repo for easier re-use.
This pipeline is designed for the collaborated study project on WHICAP cohort paper: TOBE ADDED of Reyes-Soffer Lab, Department of Preventive Medicine, Columbia University Irving Medical Center(CUIMC) and Badri Vardarajan Lab, The Gertrude H. Sergievsky Center, Department of Neurology CUIMC. We are working on Hg19 rather than the Hg38 references and originally dealing with LPA KIV2 repeats on Chr 6. So it's not exactly working the same as the source pipeline, a part of them has been modified, and the LPA-specific pipeline can be found at LPA path
Current version is the raw code intended to be run on SGE or SLURM cluster with a minimal documentation for running.
- count_read
- mosdepth
- normalize_mosdepth
- find_neighbors
- neighbors_normalization
2024/05/14: added SLURM version due to the scheduler transition of CUIMC neurology cluster from SGE to SLURM.
- Adding makefile
- Adding an argparse interface (either from cpp or python).
- Adding phasing and inputation (We have no spare valid access to UK biobank running right now)
If need any help or explanation, want to collaborate, or can help with any parts, please email Yihao Li (yl4326@cumc.columbia.edu), and CC both Dr. Gissette Reyes-Soffer (gr2104@cumc.columbia.edu) and Dr. Badri Vardarajan (bnv2103@cumc.columbia.edu).