Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-ballot built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

ValueSet: Genomic Study Data Format ValueSet

Official URL: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genomic-study-data-format-vs Version: 4.0.0-ballot
Standards status: Trial-use Maturity Level: 2 Computable Name: GenomicStudyDataFormatVS

Backport of http://hl7.org/fhir/ValueSet/genomicstudy-dataformat

References

Logical Definition (CLD)

 

Expansion

Expansion performed internally based on codesystem Genomic Study Data Format CodeSystem v4.0.0-ballot (CodeSystem)

This value set contains 40 concepts

CodeSystemDisplay (en-US)Definition
  bamhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csBAMBAM
  bedhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csBEDBED
  bedpehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csBEDPEBEDPE
  bedgraphhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csBedGraphBedGraph
  bigbedhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csbigBedbigBed
  bigWighttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csbigWigbigWig
  birdsuite-fileshttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csBirdsuite-FilesBirdsuite-Files
  broadpeakhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csbroadPeakbroadPeak
  cbshttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csCBSCBS
  chemical-reactivity-probing-profileshttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csChemical-Reactivity-Probing-ProfilesChemical-Reactivity-Probing-Profiles
  chrom-sizeshttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cschrom-sizeschrom-sizes
  cnhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csCNCN
  custom-file-formatshttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csCustom-File-FormatsCustom-File-Formats
  cytobandhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csCytobandCytoband
  fastahttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csFASTAFASTA
  gcthttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csGCTGCT
  cramhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csCRAMCRAM
  genepredhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csgenePredgenePred
  gff-gtfhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csGFF/GTFGFF/GTF
  gistichttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csGISTICGISTIC
  gobyhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csGobyGoby
  gwashttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csGWASGWAS
  igvhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csIGVIGV
  lohhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csLOHLOH
  maf-multiple-alignment-formathttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csMAF-Multiple Alignment FormatMAF-Multiple Alignment Format
  maf-mutation-annotation-formathttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csMAF-Mutation-Annotation-FormatMAF-Mutation-Annotation-Format
  merged-bam-filehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csMerged BAM FileMerged BAM File
  muthttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csMUTMUT
  narrowpeakhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csnarrowPeaknarrowPeak
  pslhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csPSLPSL
  reshttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csRESRES
  rna-secondary-structure-formatshttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csRNA-Secondary-Structure-FormatsRNA-Secondary-Structure-Formats
  samhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csSAMSAM
  sample-info-attributes-filehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csSample-Info-Attributes-fileSample-Info-Attributes-file
  seghttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csSEGSEG
  tdfhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csTDFTDF
  track-linehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csTrack LineTrack Line
  type-linehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csType LineType Line
  vcfhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csVCFVCF
  wighttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-csWIGWIG

Explanation of the columns that may appear on this page:

Level A few code lists that FHIR defines are hierarchical - each code is assigned a level. In this scheme, some codes are under other codes, and imply that the code they are under also applies
System The source of the definition of the code (when the value set draws in codes defined elsewhere)
Code The code (used as the code in the resource instance)
Display The display (used in the display element of a Coding). If there is no display, implementers should not simply display the code, but map the concept into their application
Definition An explanation of the meaning of the concept
Comments Additional notes about how to use the code