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Pediatric Germline SVs

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).


Synopsis

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).


Table of Contents

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

Helper R package

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.