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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
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SAUtils conflicting entries in custom annotation #55

Closed IvantheDugtrio closed 3 years ago

IvantheDugtrio commented 3 years ago

2021-06-10_classification_database-IAD.txt I'm having an issue creating a custom annotation with SAUtils 3.16.1-0, where I keep getting an error stating the following: conflicting entries for items at chr1:6257785 for alleles > T Deleting the notes column changes the error to a different coordinate, however neither coordinate exist in the file. Is there a parsing error with this file? See the attached.

rajatshuvro commented 3 years ago

This looks like a bug indeed. I am investigating this issue.

rajatshuvro commented 3 years ago

Hi @IvantheDugtrio , I found the issue. If you look at the range chr1:6,257,784-6,257,792 on ucsc genome browser, you will see that it is all Ts. So an insertion of T at 6257793 can be left shifted to an insertion of T at 6257785. In other words, chr1-6257792-T-TT is equivalent to chr1-6257784-C-CT. That is why, our SAUtils tool is complaining. Please remove one of them and it should work fine.

Hope this was useful.

Regards Rajat

IvantheDugtrio commented 3 years ago

Hi @rajatshuvro ,

Thanks for the help! I cleaned up the annotation file and it imports successfully now.

Thanks, Ivan