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mcovarr committed Nov 13, 2023
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4 changes: 2 additions & 2 deletions scripts/variantstore/tieout/AoU_PRECISION_SENSITIVITY.md
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## Prerequisites
1. Complete (at least) through the training step (`GvsCreateFilterSet`) of the [GVS pipeline](../docs/aou/AOU_DELIVERABLES.md) with all the samples (control and non-control).
1. Run the `GvsPrepareRanges` WDL with the following input values:
1. call_set_identifier`, `dataset_name`, `project_id` set to the same values as the inputs of the same name in the preceding `GvsCreateFilterSet` run.
1. `call_set_identifier`, `dataset_name`, `project_id` set to the same values as the inputs of the same name in the preceding `GvsCreateFilterSet` run.
1. `control_samples` set to `true`.
1. Make sure to set `use_compressed_references` to the appropriate value. This will be `true` for AoU callsets starting with Echo.
1. Run the `GvsExtractCallset` WDL with the following input values:
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```

Then all the output control VCFs might be selected into a FOFN with some globbing. Perform the following in a notebook
in the workspace and then copy the resulting FOFN to a location under the workspace bucket:
in the workspace:

```
gsutil ls 'gs://<long prefix with workspace id, submission id, etc>/call-ExtractTask/shard-*/*.vcf.gz' > vcfs_fofn.txt
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