hail.vds.impute_sex_chromosome_ploidy

hail.vds.impute_sex_chromosome_ploidy(vds, calling_intervals, normalization_contig, use_variant_dataset=False)[source]

Impute sex chromosome ploidy from depth of reference or variant data within calling intervals.

Returns a Table with sample ID keys, with the following fields:

  • autosomal_mean_dp (float64): Mean depth on calling intervals on normalization contig.

  • x_mean_dp (float64): Mean depth on calling intervals on X chromosome.

  • x_ploidy (float64): Estimated ploidy on X chromosome. Equal to 2 * x_mean_dp / autosomal_mean_dp.

  • y_mean_dp (float64): Mean depth on calling intervals on chromosome.

  • y_ploidy (float64): Estimated ploidy on Y chromosome. Equal to 2 * y_mean_db / autosomal_mean_dp.

Parameters:

  • vds (vds: VariantDataset) – Dataset.

  • calling_intervals (Table or ArrayExpression) – Calling intervals with consistent read coverage (for exomes, trim the capture intervals).

  • normalization_contig (str) – Autosomal contig for depth comparison.

  • use_variant_dataset (bool) – Whether to use depth of variant data within calling intervals instead of reference data. Default will use reference data.

Returns:

Table