feat: 438 vep annotation order #441
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…notations for VEP
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mbenary
requested changes
Sep 13, 2023
| @@ -26,7 +26,31 @@ | |||
| Step Output | |||
| =========== | |||
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| TODO | |||
| Annotations can be done on all genes & transcripts overlapping with the variant locus, or | |||
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Rephrasing:
Users can annotate all genes ...
so it fits better with the second part of the sentence.
| In the latter case, the output vcf file will only contain one annotation per variant, while | ||
| in the former case, there might be over 100 annotations for each variant. | ||
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| The ordering of features drinving the representative annotation choice is under user control. |
| @@ -115,7 +139,7 @@ | |||
| assembly: GRCh38 | |||
| cache_version: 102 # WARNING- this must match the wrapper's vep version! | |||
| tx_flag: "gencode_basic" # The flag selecting the transcripts. One of "gencode_basic", "refseq", and "merged". | |||
| pick: yes # Other option: no (report one or all consequences) | |||
| pick_order: ["biotype", "mane", "appris", "tsl", "ccds", "canonical", "rank", "length"] | |||
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Is it possible to print a constant here? If yes, one could make PICK_ORDER a global constant and reuse it for the configuration.
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This is the default order. In check_config, the code tests validity of all the options provided by the user in the yaml file
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| if selected: | ||
| for criterion in criteria: | ||
| codes[criterion] = get_value(criterion, fields[criterion]) |
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Probably a very simple thing: Why is codes changed here? It's not used afterwards.
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It's used before... The codes store the current value for the selected (best) annotation
- The codes are all set on maximum values (so the least likely to be selected).
- For each annotation, we loop over all criteria
- Get the criterion code for the current annotation
- If the code is unknown or equal to the current annotation, continue to the next criterion
- If the code is smaller than the current annotation, then this annotation is better than the selected, and should replace it.
- If the current annotation is selected, then set all codes for this annotation, and replace the selected values for the newly selected annotation values
I hope it makes sense...
This was referenced Dec 9, 2024
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Impose user-defined annotation order for VEP.
Previously, the wrapper was using the default order, based on ENSEMBL canonical transcript.
Because of that choice, many variant were not uploaded to cBioPortal.
The default choice now prioritizes protein-coding genes with MANE transcripts.
Many variants are now recovered in cBioPortal views.