hail.vds.impute_sex_chr_ploidy_from_interval_coverage

hail.vds.impute_sex_chr_ploidy_from_interval_coverage(mt, normalization_contig)[source]

Impute sex chromosome ploidy from a precomputed interval coverage MatrixTable.

The input MatrixTable must have the following row fields:

  • interval (interval): Genomic interval of interest.

  • interval_size (int32): Size of interval, in bases.

And the following entry fields:

  • sum_dp (int64): Sum of depth values by base across the interval.

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:

  • mt (MatrixTable) – Interval-by-sample MatrixTable with sum of depth values across the interval.

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

Returns:

Table