Plot SV counts at the end of the ClusterBatch module #389
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mwalker174
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Aug 19, 2022
Co-authored-by: Mark Walker <[email protected]>
mwalker174
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Oct 5, 2022
| "ClusterBatch.ped_file": {{ test_batch.ped_file | tojson }} | ||
| "ClusterBatch.ped_file": {{ test_batch.ped_file | tojson }}, | ||
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| "ClusterBatch.outlier_cutoff_nIQR": "10000" |
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Suggested change
| "ClusterBatch.outlier_cutoff_nIQR": "10000" | |
| "ClusterBatch.outlier_cutoff_nIQR": "8" |
10000 is used in FilterBatch to effectively disable sample filtering. Here we should make it something statistically reasonable, otherwise the cutoffs at +/- 10000 IQR make the plots unreadable.
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I've been using 6 for plotting
| @@ -65,6 +66,8 @@ workflow ClusterBatch { | |||
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| Float? java_mem_fraction | |||
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| Int outlier_cutoff_nIQR | |||
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I'd suggest making this an optional. If it's provided, we run PlotSVCountsPerSample. If not, it skips the task (we don't need to run this for the single sample pipeline for example). Would need to add this input and the outputs to GATKSVPipelinePhase1 and GATKSVPipelineBatch.
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This was completed as part of #567 so I would recommend closing this PR |
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The plots will be used for removing outliers before training the random forest model. This is the first step in resolving the issue #44.