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 (-v): verbose logging. This is the default.
• --quiet (-q): only log warnings and errors.
• --debug (-d): debugging mode for more verbose logging. Takes precedence over --verbose and --quiet.

Logging

Each run writes its log files to a directory next to the output VCF, named after the output file with the .vcf.gz suffix replaced by _logs, so sample.vcf.gz produces sample_logs/. The directory records the invocation in command.txt, the pipeline's own messages in run.log, and the output of each tool under task_logs/. Run metrics are also written as tab-separated tables for analysis: process_metrics.txt (one row per process, with its CPU time, peak memory and exit code) and job_metrics.txt (one row per pipeline job). Every pipeline accepts a --log_dir argument to write these files elsewhere. Rerunning a pipeline with the same output overwrites the logs of the previous run.

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.