hail.vds.sample_qc

hail.vds.sample_qc(vds, *, gq_bins=(0, 20, 60), dp_bins=(0, 1, 10, 20, 30), dp_field=None)[source]

Compute sample quality metrics about a VariantDataset.

If the dp_field parameter is not specified, the DP is used for depth if present. If no DP field is present, the MIN_DP field is used. If no DP or MIN_DP field is present, no depth statistics will be calculated.

Parameters:

  • vds (VariantDataset) – Dataset in VariantDataset representation.

  • gq_bins (tuple of int) – Tuple containing cutoffs for genotype quality (GQ) scores.

  • dp_bins (tuple of int) – Tuple containing cutoffs for depth (DP) scores.

  • dp_field (str) – Name of depth field. If not supplied, DP or MIN_DP will be used, in that order.

Returns:

Table – Hail Table of results, keyed by sample.