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Using one of the two annotation sources VCF is used when same annotation source name is used #1651
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Example of custom annotation order swapped:
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Hi @Aisha-D, Best wishes, |
The issue is in your command. In the custom annotation you use the same short name (COSMIC) for both cosmic annotations:
This name has to be unique, if you change the names to
Let me know if you have more questions. Best wishes, |
Hi Diana, |
That makes sense. We will update VEP in the future to check if there are any duplicated names. Best wishes, |
Describe the issue
If two custom annotations with the same name are provided, vep will annotate the VCF using first custom annotation and ignore the second annotation source. Expectation was an error to be raised (to require clarification to differentiate the two annotation sources).
Example of command and VCF header output:
System
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