Annotation

CWAS-Plus annotated 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.

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