dannScore and gerpScore attributes use "," instead of "." when their value is a floating point

[algarsi3]

I annotated a test VCF file using the following command:

dotnet bin/Release/net6.0/Nirvana.dll \ -c Data/Cache/GRCh37/Both \ --sd Data/SupplementaryAnnotation/GRCh37 \ -r Data/References/Homo_sapiens.GRCh37.Nirvana.dat \ -i files/out-test.vcf \ -o files/out

When inspecting the JSON file, there is a , instead of a . in gerpScore and dannScore when their value is not an integer

[rajatshuvro]

Hi @algarsi3 , We had fixed some of those issues in recent Nirvana versions. Can you share the JSON part where you see this?

Thanks Rajat

[algarsi3]

Hi, this is an example of a variation with this error:

{
  "chromosome": "chr1",
  "position": 11174383,
  "refAllele": "A",
  "altAlleles": [
    "G"
  ],
  "quality": 231394,
  "filters": [
    "PASS"
  ],
  "cytogeneticBand": "1p36.22",
  "variants": [
    {
      "vid": "1-11174383-A-G",
      "chromosome": "chr1",
      "begin": 11174383,
      "end": 11174383,
      "refAllele": "A",
      "altAllele": "G",
      "variantType": "SNV",
      "hgvsg": "NC_000001.10:g.11174383A>G",
      "phylopScore": 4.7,
      "dannScore": 1,
      "gerpScore": 5,89, <--- HERE
    }
  ]
}

[rajatshuvro]

Thanks @algarsi3 . You may track the following ticket: https://nirvana-annotator.atlassian.net/browse/NIR-1276

[algarsi3]

Hello, I see that this was solved in the 3.19 version, which is unreleased. Is there any estimated release date for the 3.19 version?

[rajatshuvro]

Hi @algarsi3 , We are still ironing our some details about the release. Thanks for your patience.

Regards Rajat

[wuttke]

How can we get the version 3.19?

[wuttke]

It is an annoying bug as no parser can read the malformed JSON. Here is how I worked around:

zcat xx.json.gz | \
        sed 's/"dannScore":\(-\?[0-9]\+\),\([0-9]\+\)/"dannScore":\1.\2/g' | \
        sed 's/"gerpScore":\(-\?[0-9]\+\),\([0-9]\+\)/"gerpScore":\1.\2/g' | \
        gzip > yy.json.gz

[rajatshuvro]

Hello @wuttke, Thank you for your interest about Nirvana. We intend to make the command line tool available. However, this will not be open-source, but it will be downloadable without any cost. Our target timeframe for this release is sometime in September. Furthermore, you can expect a lightweight license to ensure that access is granted exclusively to Illumina customers, with a requirement not to distribute these files externally.

Please share you contact information (email , organization, etc.) so that we can reach out to you.

Best regards, Rajat

[wuttke]

Hi @rajatshuvro,

thank you very much for your response.

Here is my contact information:

Matthias Wuttke, Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany; matthias.wuttke@uniklinik-freiburg.de

Thanks Matthias