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update docs on creating sample_set_set if sample_set_set table doesn'…
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epiercehoffman committed Aug 6, 2024
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Expand Up @@ -190,7 +190,10 @@ These two workflows make up FilterBatch; they are subdivided in this workspace t
#### 09-MergeBatchSites

Read the full MergeBatchSites documentation [here](https://github.com/broadinstitute/gatk-sv#merge-batch-sites).
* `09-MergeBatchSites` is a cohort-level workflow, so it is run on a `sample_set_set` containing all of the batches in the cohort. You can create this `sample_set_set` while you are launching the `09-MergeBatchSites` workflow: click "Select Data", choose "Create new sample_set_set [...]", check all the batches to include (all of the ones used in `03-TrainGCNV` through `08-FilterBatchSamples`), and give it a name that follows the **Sample ID requirements**.
* `09-MergeBatchSites` is a cohort-level workflow, so it is run on a `sample_set_set` containing all of the batches in the cohort. Navigate to the Data tab of your workspace. If there is no `sample_set_set` data table, you will need to create it. To do this, select the `sample_set` data table, then select (with the check boxes) all of the batches (`sample_set`) in your cohort. These should be the `sample_sets` that you used to run steps `03-TrainGCNV` through `08-FilterBatchSamples`. Then click the "Edit" icon above the table and choose "Save selection as set." Enter a name that follows the **Sample ID requirements**. This will create a new `sample_set_set` containing all of the `sample_sets` in your cohort. When you launch MergeBatchSites, you can now select this `sample_set_set`.

<img alt="selecting batches" title="Selecting sample_sets in the data table" src="https://i.imgur.com/E5x3qqk.png" width="400"> <img alt="creating a new set" title="Creating a new sample_set_set" src="https://i.imgur.com/pizOtX9.png" width="400">
* If there is already a `sample_set_set` data table in your workspace, you can create this `sample_set_set` while you are launching the `09-MergeBatchSites` workflow: click "Select Data", choose "Create new sample_set_set [...]", check all the batches to include (all of the ones used in `03-TrainGCNV` through `08-FilterBatchSamples`), and give it a name that follows the **Sample ID requirements**.

<img alt="creating a cohort sample_set_set" title="How to create a cohort sample_set_set" src="https://i.imgur.com/zKEtSbe.png" width="500">

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