Cryptic error message when trying to validate against beacon v2 schema #46
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Hi @mshadbolt, Can you please share your npm and node version. I am getting a different error message with |
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Sure! Here's what I get: |
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Hello!
I was attempting to try out the biovalidator but I am running into errors and not sure where I am going wrong. Thanks in advance for any help or advice you can offer!
The inputs I am using are the beacon v2 genomicVariations defaultSchema and a genomic variant from a reference beacon below.
Here is the error output I get when I try to run the CLI version of biovalidator:
{ "_id": ["62afade9676e4d25e5240835"], "variantType": ["SNP"], "alternateBases": ["T"], "frequencyInPopulations": [ { "source": ["The Genome Aggregation Database (gnomAD)"], "sourceReference": ["https://gnomad.broadinstitute.org"], "frequencies": [ { "population": ["AFR_AF"], "alleleFrequency": [-1] } ] }, { "source": ["The Genome Aggregation Database (gnomAD)"], "sourceReference": ["https://gnomad.broadinstitute.org"], "frequencies": [ { "alleleFrequency": [-1], "population": ["AMR_AF"] } ] }, { "sourceReference": ["https://gnomad.broadinstitute.org"], "source": ["The Genome Aggregation Database (gnomAD)"], "frequencies": [ { "population": ["EAS_AF"], "alleleFrequency": [-1] } ] }, { "frequencies": [ { "population": ["EUR_AF"], "alleleFrequency": [-1] } ], "source": ["The Genome Aggregation Database (gnomAD)"], "sourceReference": ["https://gnomad.broadinstitute.org"] }, { "source": ["The Genome Aggregation Database (gnomAD)"], "sourceReference": ["https://gnomad.broadinstitute.org"], "frequencies": [ { "alleleFrequency": [-1], "population": ["SAS_AF"] } ] } ], "variantLevelData": { "clinicalInterpretations": [ {} ], "phenotypicEffects": [ ["MODIFIER"] ] }, "referenceBases": ["C"], "identifiers": { "clinVarIds": [ {} ], "proteinHGVSIds": [ {} ], "genomicHGVSId": [ {} ] }, "variantInternalId": ["chr21_9411318_C_T"], "position": { "start": [ [9411317] ], "refseqId": ["21"], "end": [ [9411318] ], "assemblyId": ["hs37"] }, "molecularAttributes": { "aminoacidChanges": [ {} ], "molecularEffects": [ ["MODIFIER"] ], "geneIds": [ ["CHR_START-MIR3648-1"] ] }, "caseLevelData": [ { "biosampleId": ["NA24695"], "individualId": ["NA24695"] }, { "individualId": ["NA24694"], "biosampleId": ["NA24694"] }, { "biosampleId": ["NA24631"], "individualId": ["NA24631"] } ] }The text was updated successfully, but these errors were encountered: