I am using snpeff eff annotate on Galaxy EU in order to annotate my variants from targeted sequencing. For a few variants in some samples I encountered, that the snpeff annotation (Info-Tag “ANN”) is extended in another line, so that the values of the format column are not in the same line anymore (please see picture below). The two affected variants seem to have a tremendously long snpeff annotation.
I am wondering if there is an explanation to this and if this can be easily fixed (e.g. restricting the length of the snpeff Annotation). As this is affecting only a few variants per sample, it is not too difficult to identify them and make sure the data does not get lost. However, it is a little tricky to handle in downstream analysis sometimes though. So I would be delighted, if there might me a solution and am open for any idea.
Thanks a lot!
All the best,