sentieon-cli 1.6.3

Pipeline implementations for the Sentieon software

Sentieon CLI

A command-line interface for the Sentieon software

Install using pip (recommended)

Install the sentieon-cli into your python environment with pip:

pip install sentieon_cli

Install with docker/podman

Install the sentieon-cli through a container image:

docker pull sentieon/sentieon_cli:latest
docker run --rm -v "$PWD:/data" -w /data \
    sentieon/sentieon_cli:latest \
    sentieon-cli dnascope-pangenome --help

Installation with Poetry

Create a new python virtual environment for the project, if needed:

# Create a new venv, if needed
python3 -m venv /path/to/new/virtual/environment/sentieon_cli

# Activate the venv
source /path/to/new/virtual/environment/sentieon_cli/bin/activate

sentieon-cli uses poetry for packaging and dependency management. Initially, you will need to install poetry:

pip install poetry

Clone this repository and cd into the root directory:

git clone https://github.com/sentieon/sentieon-cli.git
cd sentieon-cli

Use poetry to install the sentieon-cli into the virtual environment:

poetry install

You can then run commands from the virtual environment:

sentieon-cli ...

Global arguments

The sentieon-cli supports the following global arguments:

• --verbose: verbose logging.
• --debug: debugging mode for more verbose logging.

Supported pipelines

• DNAscope - DNAscope pipeline implementation for germline SNV and indel calling from short read data.
• DNAscope LongRead - DNAscope LongRead pipeline implementations for germline SNV and indel calling from long read data.
• DNAscope Hybrid - DNAscope short-long-hybrid pipeline.
• DNAscope Pangenome - DNAscope pangenome alignment and variant calling. Our recommended pipeline for short-read small variant calling.

License

Unless otherwise indicated, files in this repository are licensed under a BSD 2-Clause License.