Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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-cibuild 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

## : Genomic Study Data Format CodeSystem - JSON Representation

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    {
      "resourceType" : "CodeSystem",
      "id" : "genomic-study-data-format-cs",
      "text" : {
        "status" : "generated",
        "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem genomic-study-data-format-cs</b></p><a name=\"genomic-study-data-format-cs\"> </a><a name=\"hcgenomic-study-data-format-cs\"> </a><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">bam<a name=\"genomic-study-data-format-cs-bam\"> </a></td><td>BAM</td><td>BAM</td></tr><tr><td style=\"white-space:nowrap\">bed<a name=\"genomic-study-data-format-cs-bed\"> </a></td><td>BED</td><td>BED</td></tr><tr><td style=\"white-space:nowrap\">bedpe<a name=\"genomic-study-data-format-cs-bedpe\"> </a></td><td>BEDPE</td><td>BEDPE</td></tr><tr><td style=\"white-space:nowrap\">bedgraph<a name=\"genomic-study-data-format-cs-bedgraph\"> </a></td><td>BedGraph</td><td>BedGraph</td></tr><tr><td style=\"white-space:nowrap\">bigbed<a name=\"genomic-study-data-format-cs-bigbed\"> </a></td><td>bigBed</td><td>bigBed</td></tr><tr><td style=\"white-space:nowrap\">bigWig<a name=\"genomic-study-data-format-cs-bigWig\"> </a></td><td>bigWig</td><td>bigWig</td></tr><tr><td style=\"white-space:nowrap\">birdsuite-files<a name=\"genomic-study-data-format-cs-birdsuite-files\"> </a></td><td>Birdsuite-Files</td><td>Birdsuite-Files</td></tr><tr><td style=\"white-space:nowrap\">broadpeak<a name=\"genomic-study-data-format-cs-broadpeak\"> </a></td><td>broadPeak</td><td>broadPeak</td></tr><tr><td style=\"white-space:nowrap\">cbs<a name=\"genomic-study-data-format-cs-cbs\"> </a></td><td>CBS</td><td>CBS</td></tr><tr><td style=\"white-space:nowrap\">chemical-reactivity-probing-profiles<a name=\"genomic-study-data-format-cs-chemical-reactivity-probing-profiles\"> </a></td><td>Chemical-Reactivity-Probing-Profiles</td><td>Chemical-Reactivity-Probing-Profiles</td></tr><tr><td style=\"white-space:nowrap\">chrom-sizes<a name=\"genomic-study-data-format-cs-chrom-sizes\"> </a></td><td>chrom-sizes</td><td>chrom-sizes</td></tr><tr><td style=\"white-space:nowrap\">cn<a name=\"genomic-study-data-format-cs-cn\"> </a></td><td>CN</td><td>CN</td></tr><tr><td style=\"white-space:nowrap\">custom-file-formats<a name=\"genomic-study-data-format-cs-custom-file-formats\"> </a></td><td>Custom-File-Formats</td><td>Custom-File-Formats</td></tr><tr><td style=\"white-space:nowrap\">cytoband<a name=\"genomic-study-data-format-cs-cytoband\"> </a></td><td>Cytoband</td><td>Cytoband</td></tr><tr><td style=\"white-space:nowrap\">fasta<a name=\"genomic-study-data-format-cs-fasta\"> </a></td><td>FASTA</td><td>FASTA</td></tr><tr><td style=\"white-space:nowrap\">gct<a name=\"genomic-study-data-format-cs-gct\"> </a></td><td>GCT</td><td>GCT</td></tr><tr><td style=\"white-space:nowrap\">cram<a name=\"genomic-study-data-format-cs-cram\"> </a></td><td>CRAM</td><td>CRAM</td></tr><tr><td style=\"white-space:nowrap\">genepred<a name=\"genomic-study-data-format-cs-genepred\"> </a></td><td>genePred</td><td>genePred</td></tr><tr><td style=\"white-space:nowrap\">gff-gtf<a name=\"genomic-study-data-format-cs-gff-gtf\"> </a></td><td>GFF/GTF</td><td>GFF/GTF</td></tr><tr><td style=\"white-space:nowrap\">gistic<a name=\"genomic-study-data-format-cs-gistic\"> </a></td><td>GISTIC</td><td>GISTIC</td></tr><tr><td style=\"white-space:nowrap\">goby<a name=\"genomic-study-data-format-cs-goby\"> </a></td><td>Goby</td><td>Goby</td></tr><tr><td style=\"white-space:nowrap\">gwas<a name=\"genomic-study-data-format-cs-gwas\"> </a></td><td>GWAS</td><td>GWAS</td></tr><tr><td style=\"white-space:nowrap\">igv<a name=\"genomic-study-data-format-cs-igv\"> </a></td><td>IGV</td><td>IGV</td></tr><tr><td style=\"white-space:nowrap\">loh<a name=\"genomic-study-data-format-cs-loh\"> </a></td><td>LOH</td><td>LOH</td></tr><tr><td style=\"white-space:nowrap\">maf-multiple-alignment-format<a name=\"genomic-study-data-format-cs-maf-multiple-alignment-format\"> </a></td><td>MAF-Multiple Alignment Format</td><td>MAF-Multiple Alignment Format</td></tr><tr><td style=\"white-space:nowrap\">maf-mutation-annotation-format<a name=\"genomic-study-data-format-cs-maf-mutation-annotation-format\"> </a></td><td>MAF-Mutation-Annotation-Format</td><td>MAF-Mutation-Annotation-Format</td></tr><tr><td style=\"white-space:nowrap\">merged-bam-file<a name=\"genomic-study-data-format-cs-merged-bam-file\"> </a></td><td>Merged BAM File</td><td>Merged BAM File</td></tr><tr><td style=\"white-space:nowrap\">mut<a name=\"genomic-study-data-format-cs-mut\"> </a></td><td>MUT</td><td>MUT</td></tr><tr><td style=\"white-space:nowrap\">narrowpeak<a name=\"genomic-study-data-format-cs-narrowpeak\"> </a></td><td>narrowPeak</td><td>narrowPeak</td></tr><tr><td style=\"white-space:nowrap\">psl<a name=\"genomic-study-data-format-cs-psl\"> </a></td><td>PSL</td><td>PSL</td></tr><tr><td style=\"white-space:nowrap\">res<a name=\"genomic-study-data-format-cs-res\"> </a></td><td>RES</td><td>RES</td></tr><tr><td style=\"white-space:nowrap\">rna-secondary-structure-formats<a name=\"genomic-study-data-format-cs-rna-secondary-structure-formats\"> </a></td><td>RNA-Secondary-Structure-Formats</td><td>RNA-Secondary-Structure-Formats</td></tr><tr><td style=\"white-space:nowrap\">sam<a name=\"genomic-study-data-format-cs-sam\"> </a></td><td>SAM</td><td>SAM</td></tr><tr><td style=\"white-space:nowrap\">sample-info-attributes-file<a name=\"genomic-study-data-format-cs-sample-info-attributes-file\"> </a></td><td>Sample-Info-Attributes-file</td><td>Sample-Info-Attributes-file</td></tr><tr><td style=\"white-space:nowrap\">seg<a name=\"genomic-study-data-format-cs-seg\"> </a></td><td>SEG</td><td>SEG</td></tr><tr><td style=\"white-space:nowrap\">tdf<a name=\"genomic-study-data-format-cs-tdf\"> </a></td><td>TDF</td><td>TDF</td></tr><tr><td style=\"white-space:nowrap\">track-line<a name=\"genomic-study-data-format-cs-track-line\"> </a></td><td>Track Line</td><td>Track Line</td></tr><tr><td style=\"white-space:nowrap\">type-line<a name=\"genomic-study-data-format-cs-type-line\"> </a></td><td>Type Line</td><td>Type Line</td></tr><tr><td style=\"white-space:nowrap\">vcf<a name=\"genomic-study-data-format-cs-vcf\"> </a></td><td>VCF</td><td>VCF</td></tr><tr><td style=\"white-space:nowrap\">wig<a name=\"genomic-study-data-format-cs-wig\"> </a></td><td>WIG</td><td>WIG</td></tr></table></div>"
      },
      "extension" : [
        {
          "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
          "valueCode" : "cg"
        },
        {
          "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
          "valueCode" : "informative",
          "_valueCode" : {
            "extension" : [
              {
                "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom",
                "valueCanonical" : "http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting"
              }
            ]
          }
        }
      ],
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs",
      "version" : "4.0.0-cibuild",
      "name" : "GenomicStudyDataFormatCS",
      "title" : "Genomic Study Data Format CodeSystem",
      "status" : "active",
      "experimental" : true,
      "date" : "2025-11-08T00:09:50+00:00",
      "publisher" : "HL7 International / Clinical Genomics",
      "contact" : [
        {
          "name" : "HL7 International / Clinical Genomics",
          "telecom" : [
            {
              "system" : "url",
              "value" : "http://www.hl7.org/Special/committees/clingenomics"
            },
            {
              "system" : "email",
              "value" : "cg@lists.HL7.org"
            }
          ]
        }
      ],
      "description" : "Backport of http://hl7.org/fhir/genomicstudy-dataformat",
      "jurisdiction" : [
        {
          "coding" : [
            {
              "system" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
              "code" : "001",
              "display" : "World"
            }
          ]
        }
      ],
      "caseSensitive" : true,
      "content" : "complete",
      "count" : 40,
      "concept" : [
        {
          "code" : "bam",
          "display" : "BAM",
          "definition" : "BAM"
        },
        {
          "code" : "bed",
          "display" : "BED",
          "definition" : "BED"
        },
        {
          "code" : "bedpe",
          "display" : "BEDPE",
          "definition" : "BEDPE"
        },
        {
          "code" : "bedgraph",
          "display" : "BedGraph",
          "definition" : "BedGraph"
        },
        {
          "code" : "bigbed",
          "display" : "bigBed",
          "definition" : "bigBed"
        },
        {
          "code" : "bigWig",
          "display" : "bigWig",
          "definition" : "bigWig"
        },
        {
          "code" : "birdsuite-files",
          "display" : "Birdsuite-Files",
          "definition" : "Birdsuite-Files"
        },
        {
          "code" : "broadpeak",
          "display" : "broadPeak",
          "definition" : "broadPeak"
        },
        {
          "code" : "cbs",
          "display" : "CBS",
          "definition" : "CBS"
        },
        {
          "code" : "chemical-reactivity-probing-profiles",
          "display" : "Chemical-Reactivity-Probing-Profiles",
          "definition" : "Chemical-Reactivity-Probing-Profiles"
        },
        {
          "code" : "chrom-sizes",
          "display" : "chrom-sizes",
          "definition" : "chrom-sizes"
        },
        {
          "code" : "cn",
          "display" : "CN",
          "definition" : "CN"
        },
        {
          "code" : "custom-file-formats",
          "display" : "Custom-File-Formats",
          "definition" : "Custom-File-Formats"
        },
        {
          "code" : "cytoband",
          "display" : "Cytoband",
          "definition" : "Cytoband"
        },
        {
          "code" : "fasta",
          "display" : "FASTA",
          "definition" : "FASTA"
        },
        {
          "code" : "gct",
          "display" : "GCT",
          "definition" : "GCT"
        },
        {
          "code" : "cram",
          "display" : "CRAM",
          "definition" : "CRAM"
        },
        {
          "code" : "genepred",
          "display" : "genePred",
          "definition" : "genePred"
        },
        {
          "code" : "gff-gtf",
          "display" : "GFF/GTF",
          "definition" : "GFF/GTF"
        },
        {
          "code" : "gistic",
          "display" : "GISTIC",
          "definition" : "GISTIC"
        },
        {
          "code" : "goby",
          "display" : "Goby",
          "definition" : "Goby"
        },
        {
          "code" : "gwas",
          "display" : "GWAS",
          "definition" : "GWAS"
        },
        {
          "code" : "igv",
          "display" : "IGV",
          "definition" : "IGV"
        },
        {
          "code" : "loh",
          "display" : "LOH",
          "definition" : "LOH"
        },
        {
          "code" : "maf-multiple-alignment-format",
          "display" : "MAF-Multiple Alignment Format",
          "definition" : "MAF-Multiple Alignment Format"
        },
        {
          "code" : "maf-mutation-annotation-format",
          "display" : "MAF-Mutation-Annotation-Format",
          "definition" : "MAF-Mutation-Annotation-Format"
        },
        {
          "code" : "merged-bam-file",
          "display" : "Merged BAM File",
          "definition" : "Merged BAM File"
        },
        {
          "code" : "mut",
          "display" : "MUT",
          "definition" : "MUT"
        },
        {
          "code" : "narrowpeak",
          "display" : "narrowPeak",
          "definition" : "narrowPeak"
        },
        {
          "code" : "psl",
          "display" : "PSL",
          "definition" : "PSL"
        },
        {
          "code" : "res",
          "display" : "RES",
          "definition" : "RES"
        },
        {
          "code" : "rna-secondary-structure-formats",
          "display" : "RNA-Secondary-Structure-Formats",
          "definition" : "RNA-Secondary-Structure-Formats"
        },
        {
          "code" : "sam",
          "display" : "SAM",
          "definition" : "SAM"
        },
        {
          "code" : "sample-info-attributes-file",
          "display" : "Sample-Info-Attributes-file",
          "definition" : "Sample-Info-Attributes-file"
        },
        {
          "code" : "seg",
          "display" : "SEG",
          "definition" : "SEG"
        },
        {
          "code" : "tdf",
          "display" : "TDF",
          "definition" : "TDF"
        },
        {
          "code" : "track-line",
          "display" : "Track Line",
          "definition" : "Track Line"
        },
        {
          "code" : "type-line",
          "display" : "Type Line",
          "definition" : "Type Line"
        },
        {
          "code" : "vcf",
          "display" : "VCF",
          "definition" : "VCF"
        },
        {
          "code" : "wig",
          "display" : "WIG",
          "definition" : "WIG"
        }
      ]
    }