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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
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New variants added to my annotated VCF? #72

Closed anleopa closed 2 years ago

anleopa commented 2 years ago

I have annotated a VCF that has two consecutive polymorphisms: chr2 228194480 A T chr2 228194481 G T

I have noticed that in the final result a new variant has been added with this info: chr2 228194480 AG TT

¿Why is Nirvarna doing this?

rajatshuvro commented 2 years ago

By default, Nirvana recomposes variants. You can turn this off by using the command line parameter --disable-recomposition