Import reference

fake-vcf import-reference

Import reference fasta file and extract specified chromosomes if provided.

Parameters:

reference_file_path (Path): Path to reference fasta file. reference_storage_path (Path): Where to store the references. included_chromosomes (Optional[List[str]], optional): List of chromosomes to extract from reference. If not specified, all will be imported.

Example:

To import a reference file and extract specific chromosomes: :: vcf_reference_import(“path/to/reference.fasta”, “output/directory”, included_chromosomes=[“chr1”, “chr2”])

To import a reference file without extracting specific chromosomes: :: vcf_reference_import(“path/to/reference.fasta”, “output/directory”)

Usage

$ fake-vcf import-reference [OPTIONS] REFERENCE_FILE_PATH REFERENCE_STORAGE_PATH

Arguments

• REFERENCE_FILE_PATH: Path to reference fasta file. [required]

• REFERENCE_STORAGE_PATH: Where to store the references. [required]

Options

• -c, --included_chromosomes TEXT: List of chromosomes to extract from reference, if not specified all will be imported

• --help: Show this message and exit.