gnomad_qc.v5.variant_qc.create_truth_samples_vds
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Script to create a VDS of the 8 Genomes-in-a-Bottle (GiaB) truth samples from their gVCFs.

The GiaB gVCFs were sequenced with the same protocol as the AoU v8 data and live in the
AoU control-samples bucket
(``gs://fc-aou-datasets-controlled/v8/wgs/short_read/snpindel/aux/qc/control_samples/``).
They are already reblocked, so they are passed straight into Hail's VDS combiner (no
reblocking step).

The combiner needs the per-gVCF paths up front. The truth-sample bucket cannot be
listed and the sample IDs might be sensitive, so neither the paths nor the IDs are stored
in this repo. Instead the script reads a single-column TSV manifest of gVCF paths
(``truth_samples_gvcf_paths``) by known object path.

This is intended to run in the ``batch`` environment (Hail Batch in the AoU authorization
domain), since that is where the AoU truth-sample gVCFs are readable.





.. argparse::
   :ref: gnomad_qc.v5.variant_qc.create_truth_samples_vds.get_script_argument_parser
   :prog: gnomad_qc.v5.variant_qc.create_truth_samples_vds.py



Module Functions
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.. gnomad_automodulesummary:: gnomad_qc.v5.variant_qc.create_truth_samples_vds

.. automodule:: gnomad_qc.v5.variant_qc.create_truth_samples_vds
    :exclude-members: get_script_argument_parser