Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
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Clingen reciprocalOverlap and annotationOverlap attributes use "," instead of "." when their value is a floating point #75

Closed algarsi3 closed 2 years ago

algarsi3 commented 2 years ago

I annotated a test VCF file using the following command:

dotnet bin/Release/netcoreapp3.1/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, ClinGen objects use a , instead of a . in reciprocalOverlap and annotationOverlap when their value is not 0:

{
    "clingen":[
        {
            "chromosome":"1",
            "begin":779727,
            "end":12530188,
            "variantType":"copy_number_loss",
            "id":"nsv534032",
            "clinicalInterpretation":"likely pathogenic",
            "phenotypes":["Developmental delay AND/OR other significant developmental or morphological phenotypes"],
            "observedLosses":1,
            "validated":true,
            "reciprocalOverlap":0,00365,
            "annotationOverlap":0,00365
        }
    ]
}
rajatshuvro commented 2 years ago

Has been fixed in 3.18.0 release