Ge.filter_variants#
missionbio.mosaic.ge.Ge.filter_variants
- Ge.filter_variants(min_gq: int = 30, min_dp: int = 10, min_af: float = 10) None#
Filter variants based on genotype quality, depth, and allele frequency.
- Parameters:
- min_gqint
Minimum genotype quality as calculated by the variant caller. Default is 30. Variants with genotype quality less than this value will be filtered out.
- min_dpint
Minimum read depth of the variant. Default is 10. Variants with read depth less than this value will be filtered out.
- min_affloat
Minimum allele frequency of the variant. Default is 10%. Variants with allele frequency percent less than this value will be filtered out.