gnomad_qc.v5.resources.meta

Script containing metadata related resources.

Module Functions

Script containing metadata related resources.

gnomad_qc.v5.resources.meta.low_quality_samples = ExpressionResource(path=gs://fc-secure-b25d1307-7763-48b8-8045-fcae9caadfa1/v5.0/metadata/gnomad.v5.0.low_quality_samples.he)

SetExpression containing IDs of 3 samples with an unspecified data quality issue.

For more information, see Known Issue #1 in the AoU QC document: https://support.researchallofus.org/hc/en-us/articles/29390274413716-All-of-Us-Genomic-Quality-Report.

gnomad_qc.v5.resources.meta.failing_metrics_samples = ExpressionResource(path=gs://fc-secure-b25d1307-7763-48b8-8045-fcae9caadfa1/v5.0/metadata/gnomad.v5.0.failing_genomic_metrics_samples.he)

SetExpression containing IDs of 4030 samples failing coverage hard filters and 1490 samples with non-XX/XY sex ploidies.

For more information about samples failing coverage hard filters, see docstring of get_aou_failing_genomic_metrics_samples.

gnomad_qc.v5.resources.meta.samples_to_exclude = ExpressionResource(path=gs://fc-secure-b25d1307-7763-48b8-8045-fcae9caadfa1/v5.0/metadata/gnomad.v5.0.samples_to_exclude.he)

SetExpression containing IDs of samples to exclude from v5 analysis.

Contains samples that should not have been included in the AoU v8 release (3 samples with unspecified quality issues and 4030 samples failing coverage hard filters) and 1490 samples with non-XX/XY sex ploidies.