Copyright (c) 2021-Present, Ryan L. Collins and the Talkowski Laboratory.
Distributed under terms of the MIT License (see LICENSE).
This repository contains the working code and scripts used to:
- Aggregate copy-number variant (CNV) data across technologies;
- Build genome-wide CNV mutation rate maps; and
- Compute genome-wide dosage sensitivity maps
| Directory | Description |
|---|---|
annotations/ |
Processing of genome annotations |
CMA/ |
Processing & analysis of chromosomal microarray datasets |
cromwell/ |
Resources for executing cloud workflows on Cromwell |
data/ |
Manifests of datasets used in this project |
dockerfiles/ |
Build files for Docker Images used in this project |
dsmapR/ |
Source for dsmapR R package |
integration/ |
Cross-technology integration of dosage sensitivity maps |
paper/ |
Analyses & figures for DSMap paper |
scripts/ |
Stand-alone helper scripts |
wdls/ |
Stand-alone WDL workflows |
WES/ |
Processing & analysis of whole-exome sequencing datasets |
WGS/ |
Processing & analysis of whole-genome sequencing datasets |
This repository relies heavily on the functions provided by athena, a command-line toolkit designed to support the DSMap project.
Please refer to the athena repository for more information on athena, its functions, or the Docker Image provided for its deployment.
Every analysis in this repository is intended to be run in a Docker container.
If you do not have Docker installed on your machine, it is recommended to do so prior to running any code contained herein.
In many cases, analyses were parallelized in Google Cloud using the Workflow Description Language (WDL) and the Cromwell Workflow Management System.