pandas_genomics.io.from_vcf

pandas_genomics.io.from_vcf(filename: Union[str, pathlib.Path], min_qual: float = 0, drop_filtered: bool = True)

Load genetic data from a VCF or BCF file into a DataFrame

Parameters

filename: str or Path

vcf, vcf.gz, or bcf file.

min_qual: float (default = 0)

Skip loading variants with less than this quality

drop_filtered: boolean (default = True)

Skip loading variants with a FILTER value other than “PASS”

Returns

DataFrame

Columns correspond to variants (named as {variant_number}_{variant ID}). Rows correspond to samples and index columns include sample information.