Closed prasundutta87 closed 2 years ago
Hi Prasun, thank you for using Nirvana. I have some questions before I can answer your questions.
Regards Rajat
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.
Hi @drramki-chop , Nirvana does not order the consequences. We report all consequences in arbitrary order. Hope that answered your questions.
Best Rajat
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