SNAPPY Use Case "Germline"

This repository contains the SNAPPY use case for germline data processing. Processing starts from FASTQ files, and the result are files that can be loaded into VarFish. Information on how the test data was obtained can be found here.

Setup

# Preparation
git clone --recurse-submodules git@github.com:bihealth/snappy-use-case-germline.git
cd snappy-use-case-germline
pip install -r requirements.txt

# Setup
python code/set_use_case.py

Quick Info

• License: MIT
• Copyright: 2018-2021 by Core Unit Bioinformatics (CUBI), Berlin Institute of Health