ytcheung
commented
1 year ago New clinical significance types are not supported in the current Nirvana version, you will need to modify SAUtils/InputFileParsers/ClinVar/ClinVarCommon.cs to add the new types
I get this error when trying to make new nsa and nsi files. Any idea to work around this issue?
$ dotnet ~/Nirvana/bin/Release/net6.0/SAUtils.dll clinvar --ref ~/Nirvana/Data/References/Homo_sapiens.GRCh37.Nirvana.dat --rcv ~/Nirvana/Database_development/ClinVarFullRelease_00-latest.xml.gz --vcv ~/Nirvana/Database_development/ClinVarVariationRelease_00-latest.xml.gz --out ~/Nirvana/Database_development/SupplementaryDatabase
SAUtils (c) 2022 Illumina, Inc. Stromberg, Roy, Platzer, Siddiqui, Ouyang, et al 3.18.1
ERROR: Invalid clinical significance found. Observed: uncertain risk allele
Stack trace: at SAUtils.InputFileParsers.ClinVar.ClinVarVariationReader.GetSignificances(XElement in terpretations) in H:\Nirvana\SAUtils\InputFileParsers\ClinVar\ClinVarVariationReader.cs:li ne 113 at SAUtils.InputFileParsers.ClinVar.ClinVarVariationReader.ExtractVariantRecord(XElemen t xElement) in H:\Nirvana\SAUtils\InputFileParsers\ClinVar\ClinVarVariationReader.cs:line 88 at SAUtils.InputFileParsers.ClinVar.ClinVarVariationReader.GetItems()+MoveNext() in H:\ Nirvana\SAUtils\InputFileParsers\ClinVar\ClinVarVariationReader.cs:line 43 at System.Collections.Generic.List
1..ctor(IEnumerable1 collection) at SAUtils.InputFileParsers.ClinVar.ClinVarParser.GetVariationRecords() in H:\Nirvana\S AUtils\InputFileParsers\ClinVar\ClinVarParser.cs:line 201 at SAUtils.InputFileParsers.ClinVar.ClinVarParser.GetItems() in H:\Nirvana\SAUtils\Inpu tFileParsers\ClinVar\ClinVarParser.cs:line 107 at SAUtils.CreateClinvarDb.ClinVarMain.ProgramExecution() in H:\Nirvana\SAUtils\CreateC linvarDb\ClinVarMain.cs:line 75 at CommandLine.Builders.ConsoleAppErrors.Execute(Func`1 executeMethod) in H:\Nirvana\Co mmandLine\Builders\ConsoleAppBuilder.cs:line 162