viola.read_vcf_multi

read_vcf_multi(dir_path, variant_caller, as_breakpoint, file_extension, escape_dot_files)

Read VCF files in a specified directory at the same time and return as MultiBedpe object.

Parameters

• dir_path (str) – Path to the directory containing the VCF files.

• variant_caller (str) – Let this function know which SV caller was used to create vcf file. Only “manta” is supported for now.

• as_breakpoint (bool, default False) – Convert SVTYPE=BND record into breakpoint-wise SV. The SVTYPE is predicted and can be DEL, DUP, INV, INS, TRA or BND.

• exclude_empty_cases (bool, default False) – If True, skip reading empty VCF files.

• file_extension (str or None, default 'vcf') – File extension of BEDPE files. If you want to load files with no extension, specify None.

• escape_dot_files (bool, default True) – If True, avoid reading hidden files in the directory.