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 - XML Representation

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