choosing one consequence from multiple annotation query

Illumina / Nirvana

The nimble & robust variant annotator

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choosing one consequence from multiple annotation query #43

Closed prasundutta87 closed 2 years ago

prasundutta87 commented 3 years ago

Hi,

Nirvana may annotate a variant site with multiple consequences if its associated gene has multiple transcript isoforms or that variant locus is associated with two overlapping genes. How does Nirvana decide which annotation to report first?

I also want to know in DRAGEN variant calling pipeline, only one consequence is reported for a variant site. How is that done and what is the rationale behind it?

Regards, Prasun

rajatshuvro commented 3 years ago

Hi Prasun, thank you for using Nirvana. I have some questions before I can answer your questions.

For annotations of multiple transcripts, are you talking about the ordering of the transcripts or the ordering of the consequences?
As far as we know, a DRAGEN user can ask for annotation and that produces the Nirvana JSON file. The JSON file contains all transcripts and related consequences. Can you tell me where you are observing one consequence?

Regards Rajat

drramki-chop commented 2 years ago

Thanks for this neat tool (JSON!!). I guess the question was about either ordering the consequences from the most deleterious to the least or choosing a single most deleterious consequence for a particular variant.

rajatshuvro commented 2 years ago

Hi @drramki-chop , Nirvana does not order the consequences. We report all consequences in arbitrary order. Hope that answered your questions.

Best Rajat