Annotation

CWAS-Plus2 annotates variants using VEP and its own custom annotation algorithm. The parameters of the command are as below:

  • -v, –vcf_file: Path to the input vcf file. This file could be bgzipped or not.

  • -p, –num_proc: Number of worker processes that will be used for the annotation process. By default, 1.

  • -o_dir, –output_directory: Path to the directory where the output files will be saved. By default, outputs will be saved at $CWAS_WORKSPACE.

  • –docker-mode: Run VEP using Docker (ensemblorg/ensembl-vep) instead of a local binary. With this option, a local VEP installation is not required. By default, False.

  • –vep-version: VEP version for Docker image tag (e.g. 115.0). Only used with --docker-mode. If omitted, uses latest.

cwas annotation -v INPUT.vcf -o_dir OUTPUT_DIR -p 8

To run with Docker instead of a local VEP installation:

cwas annotation -v INPUT.vcf -o_dir OUTPUT_DIR -p 8 --docker-mode --vep-version 115.0