Structural variant calling and analyses from germline whole-genome sequencing (WGS) in pediatric cancers and controls
Copyright (c) 2023-Present, Riaz Gillani, Ryan L. Collins, Jett Crowdis and the Van Allen laboratory at Dana-Farber Cancer Institute.
Distributed under terms of the GNU GPL v2.0 License (see LICENSE).
This repository contains the working code and scripts used to discover, genotype, filter, annotate, and analyze germline structural variants (SVs) from WGS across various pediatric cancer and cancer-free control cohorts.
For more information, please refer to Gillani*, Collins*, Crowdis, et al.. Rare germline structural variants increase risk for pediatric solid tumors. bioRxiv (2024).
| Directory | Description |
|---|---|
analysis/ |
Scripts and other code used for formal analysis |
config/ |
Environment & Docker configuration files |
docker/ |
Docker build files |
gatksv_scripts/ |
Stand-alone scripts for post hoc filtering and manipulation of GATK-SV callsets |
src/ |
Source code for helper packages (see below) |
sv_filtering/ |
Bash code for filtering the GATK-SV callsets |
version_changelogs/ |
README for version changelogs |
wdl/ |
Stand-alone WDL workflows |
The src/ directly contains the pre-compiled source for a helper library of R functions, PedSV.
For more documentation, see the README within the src/ subdirectory.