hail.vds.filter_chromosomes

hail.vds.filter_chromosomes(vds, *, keep=None, remove=None, keep_autosomes=False)[source]

Filter chromosomes of a VariantDataset in several possible modes.

Notes

There are three modes for filter_chromosomes(), based on which argument is passed to the function. Exactly one of the below arguments must be passed by keyword.

  • keep: This argument expects a single chromosome identifier or a list of chromosome identifiers, and the function returns a VariantDataset with only those chromosomes.

  • remove: This argument expects a single chromosome identifier or a list of chromosome identifiers, and the function returns a VariantDataset with those chromosomes removed.

  • keep_autosomes: This argument expects the value True, and returns a dataset without sex and mitochondrial chromosomes.

Parameters:

  • vds (VariantDataset) – Dataset.

  • keep – Keep a specified list of contigs.

  • remove – Remove a specified list of contigs

  • keep_autosomes – If true, keep only autosomal chromosomes.

Returns:

VariantDataset.