NIRVANA output missing genes.hgncid

[LeeTL1220]

Version: 3.14 from docker image. Reference: hg38 Updated datasources using the Download tool in NIRVANA? Yes, from the same docker image (tag 3.14).

According to the documentation, the NIRVANA output should have a genes.hgncid field (the HGNC ID number, not gene symbol). This is not the geneId field, which is based on NCBI.

"genes":[
   {
      "name":"MSH6",
      "hgncId":7329,
...

(Above is a snippet from https://illumina.github.io/NirvanaDocumentation/file-formats/nirvana-json-file-format#genes)

However, in my output no gene has this. E.g.

"genes": [
    {
      "name": "AJAP1",
      "omim": [
        {
          "mimNumber": 610972,
          "geneName": "Adherens junction-associated protein 1"
        }
      ],
      "gnomAD": {
        "pLi": 0.995,
        "pRec": 0.00531,
        "pNull": 5.54e-07,
        "synZ": 0.163,
        "misZ": 0.936,
        "loeuf": 0.192
      }
    },
...

I do not see a hgncid field in any part of the output.

Thanks for any help.

[LeeTL1220]

I thought I would ping, just to ask whether this was going to be corrected in the next version of NIRVANA or whether the documentation was going to be updated to match the actual output. Or whether I am just missing something obvious? Any help is appreciated.

[snalty]

I would also like some clarity on this.

[rajatshuvro]

Hi @snalty , @LeeTL1220 , Please follow the instructions here (https://illumina.github.io/IlluminaConnectedAnnotationsDocumentation/introduction/getting-started) to get the latest version of Nirvana (now called Illumina Connected Annotations) and let us know if the problem persists.

Thanks

[snalty]

Hi @rajatshuvro,

I found this through my own searches this afternoon and this is great thanks, works perfectly and shows the hgncId in the genes section of the json.

BW