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 noDP
field is present, theMIN_DP
field is used. If noDP
orMIN_DP
field is present, no depth statistics will be calculated.- Parameters
vds (
VariantDataset
) – Dataset in VariantDataset representation.name (
str
) – Name for resulting field.gq_bins (
tuple
ofint
) – Tuple containing cutoffs for genotype quality (GQ) scores.dp_bins (
tuple
ofint
) – 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.