gnomad_qc.v5.resources.variant_qc
Script containing variant QC related resources for v5.
Module Functions
Path to a single-column TSV listing the GCS path to each truth-sample gVCF (one per line). |
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Return the path to the truth-samples VDS combiner plan (combiner |
Script containing variant QC related resources for v5.
- gnomad_qc.v5.resources.variant_qc.truth_samples_gvcf_paths = 'gs://fc-11093c2b-590e-424a-91ac-0cc040d562fc/v5.0/variant_qc/genomes/aou/truth_samples/truth_samples_gvcf_paths.tsv'
Path to a single-column TSV listing the GCS path to each truth-sample gVCF (one per line).
The truth samples are 8 Genomes-in-a-Bottle (GiaB) samples sequenced with the same protocol as the AoU v8 data. Their gVCFs are stored here: gs://fc-aou-datasets-controlled/v8/wgs/short_read/snpindel/aux/qc/control_samples/
The sample IDs are intentionally not stored in this repo. The combiner therefore reads the gVCF paths from this manifest by known object paths rather than globbing the bucket.
- gnomad_qc.v5.resources.variant_qc.truth_samples_vds = VariantDatasetResource(path=gs://fc-11093c2b-590e-424a-91ac-0cc040d562fc/v5.0/variant_qc/genomes/aou/truth_samples/truth_samples.vds)
VDS containing 8 GiaB samples.
This resource does not need to be remade for future versions.
- gnomad_qc.v5.resources.variant_qc.get_truth_samples_combiner_plan(test=False)[source]
Return the path to the truth-samples VDS combiner plan (combiner
save_path).The plan lets a failed or interrupted combiner run be resumed. It is written to the writable batch variant QC tree (or a temp path for tests).
Like truth_samples_vds, this resource does not need to be remade for future versions.
- Parameters:
test (
bool) – Whether to return a temporary test path. Default is False.- Return type:
str- Returns:
Path to the combiner plan JSON.