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VS-1483 Update AoU documentation to include details for VAT delivery #8967

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merged 7 commits into from
Sep 9, 2024
Merged

VS-1483 Update AoU documentation to include details for VAT delivery #8967

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1dc7c52
Update documentation to include steps for delivery of VAT to AoU RWB.
gbggrant Aug 28, 2024
27f6130
Updates per code review feedback.
gbggrant Aug 30, 2024
5a160ec
Merge remote-tracking branch 'origin/ah_var_store' into gg_VS-1483_Up…
gbggrant Sep 4, 2024
1c22248
Update documentation to point to Google doc describing deliverables f…
gbggrant Sep 4, 2024
36064c3
Minor syntax change
gbggrant Sep 4, 2024
017053c
Merge remote-tracking branch 'origin/ah_var_store' into gg_VS-1483_Up…
gbggrant Sep 9, 2024
d826270
Code review input
gbggrant Sep 9, 2024
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14 changes: 13 additions & 1 deletion scripts/variantstore/docs/aou/AOU_DELIVERABLES.md
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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>kevin.levy@pmi-ops.org</li>
<li>srushti.gangireddy@pmi-ops.org</li>
<li>brian.freeman@pmi-ops.org </li>
<li>tarek.ahmed@pmi-ops.org</li>
<li>jennifer.zhang@pmi-ops.org</li>
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do we really want to put these emails in our docs?

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Yeah - probably shouldn't but wasn't sure how to capture this level of detail.

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maybe link back to a Confluence or something?

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I've linked to a Google Doc that tracks what we did for Echo

</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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Suggested change
- 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.)
- 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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