Release 4 5 Snapshot #1

This page is part of the FHIR Specification (v4.0.1: R4 - Mixed Normative and STU ) in it's permanent home (it will always be available at this URL). (v5.0.0-snapshot1: Release 5 Snapshot #1). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions . Page versions: R4B R4 R3

Sequence-example-fda-vcfeval

Clinical Genomics Work Group Maturity Level : N/A Standards Status : Informative Compartments : Patient

This is the narrative for the resource. See also the XML , JSON or Turtle format. This example conforms to the profile MolecularSequence .

Generated Narrative with Details

id : fda-vcfeval-comparison

Resource "fda-vcfeval-comparison"

coordinateSystem : 1

patient : Patient/example "Peter CHALMERS"

ReferenceSeqs

- ReferenceSeqId Strand WindowStart WindowEnd
* NC_000001.11 (Details : {http://www.ncbi.nlm.nih.gov/nuccore code 'NC_000001.11' = 'NC_000001.11) (nuccore#NC_000001.11) watson 10453 101770080

Variants

- Start End ObservedAllele ReferenceAllele
* 13116 13117 T G

quality

type : indel

standardSequence : file-BkZxBZ00bpJVk2q6x43b1YBx (Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx) (#file-BkZxBZ00bpJVk2q6x43b1YBx)

start : 10453

end : 101770080

method : Vcfeval + Hap.py Comparison (Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZzZxbzZxP725P) (#app-BxfGF8j02pBZzZxbzZxP725P)

truthTP : 7749

truthFN : 2554

queryFP : 10670

gtFP : 2186

precision : 0.428005

recall : 0.752111

quality

type : snp

standardSequence : file-BkZxBZ00bpJVk2q6x43b1YBx (Details : {https://precision.fda.gov/files/ code 'file-BkZxBZ00bpJVk2q6x43b1YBx' = 'file-BkZxBZ00bpJVk2q6x43b1YBx) (#file-BkZxBZ00bpJVk2q6x43b1YBx)

start : 10453

end : 101770080

method : Vcfeval + Hap.py Comparison (Details : {https://precision.fda.gov/apps/ code 'app-BxfGF8j02pBZzZxbzZxP725P' = 'app-BxfGF8j02pBZzZxbzZxP725P) (#app-BxfGF8j02pBZzZxbzZxP725P)

truthTP : 92106

truthFN : 1247

queryFP : 21744

gtFP : 493

precision : 0.808602

recall : 0.986642

Repositories

- Type Url Name
* login https://precision.fda.gov/jobs/job-ByxYPx809jFVy21KJG74Jg3Y FDA

 

 

Usage note: every effort has been made to ensure that the examples are correct and useful, but they are not a normative part of the specification.