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extract_variants.rst

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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.

If you have too many categories to extract, -c_set option will take a while. In this case, try without -c_set option and then filter variants based on the annotation you desire.

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_set, --category_set: 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_set CATEGORY_SET.txt -ai