The Germline Genomics of Cancer (G2C)

Variant calling from germline whole-genome sequencing (WGS) across cancer types

Copyright (c) 2023-Present, Ryan L. Collins, Noah Fields, and the Van Allen, Gusev, and Haigis laboratories at Dana-Farber Cancer Institute.
Distributed under terms of the GNU GPL v2.0 License (see LICENSE).

Note: this repository is under active development. More documentation will be added as the project evolves.

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Synopsis

This repository contains the working code and scripts used to detect, genotype, filter, and annotate germline variants from germline WGS across cancer types

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Table of Contents

Directory	Description
docker/	Instructions for building project-related Docker images
scripts/	Stand-alone scripts called by various workflows
shell/	Shell snippets for running specific processes or analyses
wdl/	Stand-alone WDL workflows

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Storage

All sample-level input data is stored in a secure Google Cloud bucket. Note that permissions must be granted for bucket access.

The bucket is organized as follows:

• One directory per cohort
• Each cohort has the following subdirectories:
  • gatk-hc/reblocked : reblocked GATK-HC gVCFs and indexes
  • gatk-sv : evidence and metrics files collected by GATK-SV
    • gatk-sv/coverage : coverage counts files
    • gatk-sv/metrics : per-sample metrics generated during GATK-SV module 01
    • gatk-sv/pesr : PE/SR metadata files
  • manta : raw Manta VCFs and indexes
  • melt : raw MELT VCFs and indexes
  • wham : raw Wham VCFs and indexes

Note: all raw gVCFs previously hosted in gatk-hc/ were deleted on Feb 7, 2024, but the nested directory structure of gatk-hc/reblocked/ was preserved for legacy code compatability