Extract variants

This process is to extract variants that are allocated to a specific category. When there is a category of interest, the users can extract the variants that belong to the category and look through.

The parameters of the command are as below:

• -i, –input_file: Path to the annotated VCF, resulted from annotation process. This file should be gzipped.

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

• -t, –tag: Tag used for the name of the output file. By default, None.

• -c, –category_set_path: Path to a txt file containing categories for extracting variants. By default, None. This file must contain Category column with the name of categories to be extracted.

  Category
  All_CHD8Common_All_IntergenicRegion_EarlyCREMicro
  All_CHD8Common_phastCons46way_PromoterRegion_EarlyCREL4
  All_DDD_All_PromoterRegion_EarlyCREOligo

• -ai, –annotation_info: Saves with annotation information attached (such as gene list, functional annotations, etc). By default, False.

Without a category set

cwas extract_variant -i INPUT.annotated.vcf.gz -o_dir OUTPUT_DIR -t filtered -ai

With a category set

cwas extract_variant -i INPUT.annotated.vcf.gz -o_dir OUTPUT_DIR -t filtered -ai -c CATEGORY_SET.txt -ai