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How to run 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.
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:
export PYTHONPATH="path2repository/GenOtoScope:$PYTHONPATH"
- Activate ~.bashrc:
source ~.bashrc
-
-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
Given megSAP is installed in a docker with root path: /home/username/dockerspace and docker image id XYZ
- 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
- 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