BashGATK

Bash implementation of GATK-based analysis, designed specifically for paired targeted NGS.

Installation

Install GNU parallel (please reference the original work):

Install Docker and DeepVariant to use it:

Get user into the docker group:

Reboot afterwards.

Install conda environments using the corresponding yml-files in the root directory of this repository:

• ppp_genebe
• ppp_oc
• ppp_proc
• ppp_spliceai

For example,

GeneBe

Create the .netrc file to use genebe, then change permissions:

OpenCRAVAT

Start the

environment, then run the following commands:

Parquet output

To output parquet files along with the excel-outputs you will need to install pyarrow, which might conflict being installed via conda in the ppp_spliceai environment.

However, if the pyarrow package is installed via pip in the ppp_spliceai environment, it might work. Version 21.0.0 works all right.

You also will need to create a bash variable doParquetFlag='y'.

Pipeline example

Pipeline example is in the main_example.sh file.

Usage: