Add v4 variant QC annotation HT creation and true positive VCF export #402
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…to jg/v4_export_tp_vcfs
…to jg/v4_random_forest_annotation_ht # Conflicts: # gnomad_qc/v4/annotations/generate_variant_qc_annotations.py
…to jg/v4_random_forest_annotation_ht # Conflicts: # gnomad_qc/v4/annotations/generate_variant_qc_annotations.py
| positive variants. | ||
| :return: Dictionary of 'raw' and 'adj' true positive variant Tables. | ||
| """ | ||
| if not transmitted_singletons and not sibling_singletons: |
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Conceptual question - why does this have to be the case? Why can't the true positives not include singletons?
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Just adding to clarify what we are making. Want to make two files (there is also an option for a 3rd, but we probably won't test it, so no reason to make it).
- VCF of just transmitted singletons: These are determined by looking at the trios and identifying variants that are found in one parent and the child, and those two individuals are the only two in the callset with the variant.
- VCF of transmitted singletons (defined above) and sibling singletons: sibling singletons are determined by looking at two individuals that are siblings and identifying variants that are found in both siblings, and these two individuals are the only individuals in the callset with that variant.
- We can also export just sibling singletons, but it's not really worth it.
We use these as true positives in the variant QC training so that we can see what the features we use in the model look like on rare variants that we have high confidence in being real.
This if statement is just throwing an error because if you don't pick one of these you are just asking for an empty VCF
| ) -> PipelineResourceCollection: | ||
| """ | ||
| Get PipelineResourceCollection for all resources needed in the variant QC annotation pipeline. | ||
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| :param test: Whether to gather all resources for testing. | ||
| :param overwrite: Whether to overwrite resources if they exist. | ||
| :param true_positive_type: Type of true positive variants to use for true positive | ||
| VCF path resource. Default is None. |
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| VCF path resource. Default is None. | |
| VCF path resource when exporting. Default is None. |
A bit unclear abt code - does it not export the True Positive VCFs if this isn't passed? If so, may want to mention in params. If I'm just misreading it though, then nvm
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get_variant_qc_annotation_resources is only getting the resources and not actually performing the export
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ah sorry, makes sense now
Co-authored-by: Daniel Marten <[email protected]>
| ) -> PipelineResourceCollection: | ||
| """ | ||
| Get PipelineResourceCollection for all resources needed in the variant QC annotation pipeline. | ||
|
|
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| :param test: Whether to gather all resources for testing. | ||
| :param overwrite: Whether to overwrite resources if they exist. | ||
| :param true_positive_type: Type of true positive variants to use for true positive | ||
| VCF path resource. Default is None. |
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ah sorry, makes sense now
| tp_vcf_args.add_argument( | ||
| "--export-true-positive-vcfs", | ||
| help=( | ||
| "Exports true positive variants (--transmitted-singletons and/or" | ||
| " --sibling-singletons) to VCF files." | ||
| ), | ||
| action="store_true", | ||
| ) |
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Is there ever a use case where either --transmitted-singletons and/or --sibling-singletons are passed but not --export-true-positives-vcfs ? Do they, or the PipelineStepResourceCollection named 'export_true_positive_vcfs', have any other function in the code or are read in elsewhere ?
If there isn't, you could just choose to export if either true positive types are passed - it would cut down on arguments but might be less user-friendly when passing argument.
Think the only code change would be changing line #668 to if true_positive_type: , but only if this is the case
…to jg/v4_random_forest_annotation_ht # Conflicts: # gnomad_qc/v4/annotations/generate_variant_qc_annotations.py
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