Impact not in json file

[oshiomah1]

Hello,

I ran NIRVANA on a whole genome sequence on chromosme 10(human). It ran with no errors and the output seems similar to the tutorial but I notice that the impact from snpeff/vep which should be in the transcripts section doesn't show up here's andn example"transcripts":[{"transcript":"ENST00000443774.5","source":"Ensembl","bioType":"protein_coding","codons":"Gat/Aat","aminoAcids":"D/N","cdnaPos":"75","cdsPos":"25","exons":"1/4","proteinPos":"9","geneId":"ENSG00000225899","hgnc":"FRG2B","consequence":["missense_variant"],"hgvsc":"ENST00000443774.5:c.25G>A","hgvsp":"ENSP00000408343.1:p.(Asp9Asn)","isCanonical":true,"polyPhenScore":0.57,"polyPhenPrediction":"possibly damaging","proteinId":"ENSP00000408343.1","siftScore":0.17,"siftPrediction":"tolerated"}

[rajatshuvro]

Hi @oshiomah1 , The Nirvana project is no longer active. We are working on a replacement from Illumina. Please share your contacts and we will get back to you when the release is ready.

Thanks Rajat

[oshiomah1]

Hello,

My email is @.***

Looking forward to hearing back from you soon!

Best, Oshiomah Oyageshio

On Tue, Nov 7, 2023 at 9:05 AM Rajat Shuvro Roy @.***> wrote:

Closed #117 https://github.com/Illumina/Nirvana/issues/117 as completed.

— Reply to this email directly, view it on GitHub https://github.com/Illumina/Nirvana/issues/117#event-10889787004, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARAL2AMD4A3CWLMAOV6MOJTYDJS5LAVCNFSM6AAAAAA65AZJTGVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJQHA4DSNZYG4YDANA . You are receiving this because you were mentioned.Message ID: @.***>

--

Oshiomah Oyageshio University of California - Davis Population Biology | PhD Student Henn Lab for Population Genetics http://hennlab.ucdavis.edu/ Twitter: @OshiomahO https://twitter.com/oshiomaho?s=11

[rajatshuvro]

Hi @oshiomah1 , your email address above has been masked out.

[oshiomah1]

sorry about that it is Oyageshio@ucdavis.edu oyageshio[at]ucdavis[dot]edu.