How to run genotoscope_annotate.py

genotoscope_annotate.py

This command accepts as input a VCF file (single WES) or a set of VCF files (WES for a set of patients).

It annotates the VCF files by VeP using the megSAP bioinformatics suite.

It outputs the annotated file(s) in GSvar format.

How to setup megSAP

To run this command you need to install the megSAP in docker container.

• install the docker container using the dockerfile found in the megSAP repository
• start the container
• get the container image id: docker ps --latest

Add in bashrc

• Add in ~.bashrc: export PYTHONPATH="path2repository/GenOtoScope:$PYTHONPATH"
• Activate ~.bashrc: source ~.bashrc

Options

• -h, --help show this help message and exit
• --input_variants INPUT_VARIANTS |String| Absolute path to patients variants or single file path with variants
• --output_path OUTPUT_PATH |String| Absolute path to output directory (it will be created, if not existing)
• --docker_root DOCKER_ROOT |String| Name of mounted docker root directory
• --docker_root_host DOCKER_ROOT_HOST |String| Absolute path to docker directory in host
• --docker_image_id DOCKER_IMAGE_ID |String| Configured docker image ID
• --logging {INFO} |String| Logging level

Example runs

Given megSAP is installed in a docker with root path: /home/username/dockerspace and docker image id XYZ

1. Annotate all vcf files in given folder: /home/username/example_vcfs and output folder: /home/username/example_vcfs_annotate

python3.7 genotoscope_annotate.py --input_variants /home/username/example_vcfs --output_path /home/username/example_vcfs_annotate --docker_root /megSAP --docker_root_host /home/username/dockerspace --docker_image_id XYZ --logging INFO > /home/username/annotate.out 2> /home/username/annotate.error

2. Annotate a specific vcf file: /home/username/example_vcfs/example_vars.vcf and output folder:/home/username/example_vcfs_annotate

python3.7 genotoscope_annotate.py --input_variants /home/username/example_vcfs/example_vars.vcf --output_path /home/username/example_vcfs_annotate --docker_root /megSAP --docker_root_host /home/username/dockerspace --docker_image_id XYZ --logging INFO > /home/username/annotate_single_file.out 2> /home/username/annotate_single_file.error