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Rc vs 1036 updating docs for callset creation #8600

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Rc vs 1036 updating docs for callset creation #8600

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3e166d9
update documentation for validation script
RoriCremer Dec 5, 2023
3087989
alt allele table is cumulative now
RoriCremer Dec 7, 2023
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2 changes: 1 addition & 1 deletion scripts/variantstore/docs/aou/AOU_DELIVERABLES.md
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Expand Up @@ -57,9 +57,9 @@
- Run if there are any samples to withdraw from the last callset.
1. **TBD Workflow to soft delete samples**
1. `GvsPopulateAltAllele` workflow
- **TODO:** needs to be made cumulative so that it can add data to the existing table instead of creating it from scratch on each run (see [VS-52](https://broadworkbench.atlassian.net/browse/VS-52))
- This step loads data into the `alt_allele` table from the `vet_*` tables in preparation for running the filtering step.
- This workflow does not use the Terra Data Entity Model to run, so be sure to select the `Run workflow with inputs defined by file paths` workflow submission option.
- This step is cumulative (as are all of the steps prior), and it is the last step that is--so be sure that all samples have been loaded or withdrawn before progressing to the next step
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@RoriCremer RoriCremer Dec 7, 2023 •
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am I lying??

if data is loaded into the alt allele table for a specific sample, and then that exact sample is withdrawn later...how do we adjust the alt allele table to be sure that the sample is not used in the filter model?

1. `GvsCreateFilterSet` workflow
- This step calculates features from the `alt_allele` table, and trains the VETS filtering model along with site-level QC filters and loads them into BigQuery into a series of `filter_set_*` tables.
- See [naming conventions doc](https://docs.google.com/document/d/1pNtuv7uDoiOFPbwe4zx5sAGH7MyxwKqXkyrpNmBxeow) for guidance on what to use for `filter_set_name`, which you will need to keep track of for the `GvsExtractAvroFilesForHail` WDL. If, for some reason, this step needs to be run multiple times, be sure to use a different `filter_set_name` (the doc has guidance for this, as well).
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2 changes: 1 addition & 1 deletion scripts/variantstore/docs/aou/vds/Creating a VDS.md
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Expand Up @@ -26,7 +26,7 @@ NOTE: in the WDL created to run this script, the temp directory can be easily de

## Validate the VDS to ensure that it is ready to be shared

Copy the [VDS Validation python script](vds_validation.py) to the notebook environment.
Copy the [VDS Validation python script](../../../wdl/extract/vds_validation.py) to the notebook environment.
Run it with the following arguments:

`--vds-path`: the GCS path to the newly-created VDS
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64 changes: 0 additions & 64 deletions scripts/variantstore/docs/aou/vds/vds_validation.py
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