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Update documentation to include steps for delivery of VAT to AoU RWB.
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@@ -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) | ||
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The pipeline takes in the VDS and outputs a variant annotations table in BigQuery. | ||
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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. | ||
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- 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.) | ||
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## Additional Deliverables | ||
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### Smaller Interval Lists | ||
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