Document AoU SOP (up to the VAT) [VS-63] #7807
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mcovarr
reviewed
Apr 25, 2022
| 4. the "cohort_extract_table_prefix" input from `GvsExtractCallset` step | ||
| 5. the "filter_set_name" input from `GvsCreateFilterSet` step | ||
| ## Prerequisites | ||
| - If this is the first time running the GVS pipeline in a particular Google billing project, use your GCP account team to create a support ticket for the BigQuery team that includes "enabling cluster metadata pruning support for the BQ Read API." This enables a pre-GA feature that dramatically reduces the amount of data scanned reducing both cost and runtime. |
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"enabling cluster metadata pruning support for the BQ Read API" means autopoking?
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Actually, this is a separate issue (otherwise referred to as "whitelisting"). I need to confirm that this has been resolved.
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It's a term that Google uses, I believe it means "General Audience".
Codecov Report
@@ Coverage Diff @@
## ah_var_store #7807 +/- ##
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Coverage ? 86.295%
Complexity ? 35191
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Files ? 2170
Lines ? 164837
Branches ? 17775
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Hits ? 142246
Misses ? 16265
Partials ? 6326 |
RoriCremer
reviewed
Apr 25, 2022
gbggrant
approved these changes
Apr 26, 2022
| 4. the "cohort_extract_table_prefix" input from `GvsExtractCallset` step | ||
| 5. the "filter_set_name" input from `GvsCreateFilterSet` step | ||
| ## Prerequisites | ||
| - If this is the first time running the GVS pipeline in a particular Google billing project, use your GCP account team to create a support ticket for the BigQuery team that includes "enabling cluster metadata pruning support for the BQ Read API." This enables a pre-GA feature that dramatically reduces the amount of data scanned reducing both cost and runtime. |
Co-authored-by: George Grant <[email protected]>
mcovarr
approved these changes
Apr 26, 2022
| 4. GvsCreateAltAllele | ||
| 5. GvsCreateFilterSet (see [naming conventions doc](https://docs.google.com/document/d/1pNtuv7uDoiOFPbwe4zx5sAGH7MyxwKqXkyrpNmBxeow) for guidance on what to name the filter set, which you will need to keep track of for the `GvsExtractCallset` WDL). | ||
| 6. GvsPrepareRangesCallset needs to be run twice, once with `control_samples` set to "true" (see [naming conventions doc](https://docs.google.com/document/d/1pNtuv7uDoiOFPbwe4zx5sAGH7MyxwKqXkyrpNmBxeow) for guidance on what to use for `extract_table_prefix` or cohort prefix, which you will need to keep track of for the `GvsExtractCallset` WDL). | ||
| 7. GvsExtractCallset needs to be run twice, once with `control_samples` set to "true", and with the `filter_set_name` and `extract_table_prefix` from step 5 & 6. Include a valid (and secure) "output_gcs_dir" parameter, which is where the VCF and interval list files will go. |
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Suggested change
| 7. GvsExtractCallset needs to be run twice, once with `control_samples` set to "true", and with the `filter_set_name` and `extract_table_prefix` from step 5 & 6. Include a valid (and secure) "output_gcs_dir" parameter, which is where the VCF and interval list files will go. | |
| 7. GvsExtractCallset needs to be run twice, once with `control_samples` set to "true", and with the `filter_set_name` and `extract_table_prefix` from step 5 & 6. Include a valid (and secure) "output_gcs_dir" parameter, which is where the VCF and interval list files will go. |
This was referenced Mar 17, 2023
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