07:14:36 [main] WARN org.cbioportal.annotator.internal.GenomeNexusImpl - Annotated record is invalid for variant 17:7578213-7578213:1/A
Yet the ANNOTATION_STATUS == SUCCESS. This is slightly peculiar, it should probably indicate a fail if the annotated record is invalid.
However the real issue is the following: 7578213 is not G at that position. But using region format we don't supply the inputted reference allele, so technically we would still annotate it and VEP would not fail. One would have to compare the resulting referenceAllele against the inputted reference allele and throw a failure if they don't match.
It seems like we still try to annotate mutations even when the annotation failed, see:
https://github.com/genome-nexus/annotation-tools/issues/31
For instance for this case:
The annotation pipeline might use this endpoint:
https://genie.genomenexus.org/annotation/17:g.7578213G%3EA?fields=annotation_summary&isoformOverrideSource=uniprot
and throws a warning:
Yet the
ANNOTATION_STATUS == SUCCESS. This is slightly peculiar, it should probably indicate a fail if the annotated record is invalid.However the real issue is the following: 7578213 is not G at that position. But using region format we don't supply the inputted reference allele, so technically we would still annotate it and VEP would not fail. One would have to compare the resulting referenceAllele against the inputted reference allele and throw a failure if they don't match.