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Update documentation to include steps for delivery of VAT to AoU RWB.
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gbggrant committed Aug 28, 2024
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Expand Up @@ -99,9 +99,21 @@ The Callset Stats and S&P files can be simply `gsutil cp`ed to the AoU delivery
## Running the VAT pipeline
To create a BigQuery table of variant annotations, you may follow the instructions here:
[process to create variant annotations table](../../variant_annotations_table/README.md)

The pipeline takes in the VDS and outputs a variant annotations table in BigQuery.

Once the VAT table and a tsv is exported, the AoU research workbench team should be notified of its creation and permission should be granted so that several members of the team have view permission.

- Grant `BigQuery Data Viewer` permission to specific people's PMI-OPS accounts. As of the Echo release, these accounts were:
<ul>
<li>[email protected]</li>
<li>[email protected]</li>
<li>[email protected] </li>
<li>[email protected]</li>
<li>[email protected]</li>
</ul>
- Copy the bgzipped, tarred export of the VAT into the pre-delivery bucket. For the Echo release, it was copied to `gs://prod-drc-broad/v8/wgs/vat/aou_srwgs_short_variants_v8r1.vat.bgz.tsv.gz`
- Finally, an email should be sent out notifying the AoU research workbench team (and others) of the readiness of the VAT. For echo, the email had the subject line: `Variant Annotations Table delivered for v8 srWGS joint callset` (it may just be easiest to find that email and modify it accordingly for the release you are working on.)

## Additional Deliverables

### Smaller Interval Lists
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