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