This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions
Active as of 2024-12-12 |
<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><a name="genomic-study-data-format-cs-en-US"> </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></tr><tr><td style="white-space:nowrap">bam<a name="genomic-study-data-format-cs-bam"> </a></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></tr><tr><td style="white-space:nowrap">bedpe<a name="genomic-study-data-format-cs-bedpe"> </a></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></tr><tr><td style="white-space:nowrap">bigbed<a name="genomic-study-data-format-cs-bigbed"> </a></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></tr><tr><td style="white-space:nowrap">birdsuite-files<a name="genomic-study-data-format-cs-birdsuite-files"> </a></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></tr><tr><td style="white-space:nowrap">cbs<a name="genomic-study-data-format-cs-cbs"> </a></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></tr><tr><td style="white-space:nowrap">chrom-sizes<a name="genomic-study-data-format-cs-chrom-sizes"> </a></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></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></tr><tr><td style="white-space:nowrap">cytoband<a name="genomic-study-data-format-cs-cytoband"> </a></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></tr><tr><td style="white-space:nowrap">gct<a name="genomic-study-data-format-cs-gct"> </a></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></tr><tr><td style="white-space:nowrap">genepred<a name="genomic-study-data-format-cs-genepred"> </a></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></tr><tr><td style="white-space:nowrap">gistic<a name="genomic-study-data-format-cs-gistic"> </a></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></tr><tr><td style="white-space:nowrap">gwas<a name="genomic-study-data-format-cs-gwas"> </a></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></tr><tr><td style="white-space:nowrap">loh<a name="genomic-study-data-format-cs-loh"> </a></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></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></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></tr><tr><td style="white-space:nowrap">mut<a name="genomic-study-data-format-cs-mut"> </a></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></tr><tr><td style="white-space:nowrap">psl<a name="genomic-study-data-format-cs-psl"> </a></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></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></tr><tr><td style="white-space:nowrap">sam<a name="genomic-study-data-format-cs-sam"> </a></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></tr><tr><td style="white-space:nowrap">seg<a name="genomic-study-data-format-cs-seg"> </a></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></tr><tr><td style="white-space:nowrap">track-line<a name="genomic-study-data-format-cs-track-line"> </a></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></tr><tr><td style="white-space:nowrap">vcf<a name="genomic-study-data-format-cs-vcf"> </a></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></tr></table></div>
</text>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
<valueCode value="cg"/>
</extension>
<url
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs"/>
<version value="3.0.0"/>
<name value="GenomicStudyDataFormatCS"/>
<title value="Genomic Study Data Format CodeSystem"/>
<status value="active"/>
<experimental value="true"/>
<date value="2024-12-12T20:43:36+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"/>
</concept>
<concept>
<code value="bed"/>
<display value="BED"/>
</concept>
<concept>
<code value="bedpe"/>
<display value="BEDPE"/>
</concept>
<concept>
<code value="bedgraph"/>
<display value="BedGraph"/>
</concept>
<concept>
<code value="bigbed"/>
<display value="bigBed"/>
</concept>
<concept>
<code value="bigWig"/>
<display value="bigWig"/>
</concept>
<concept>
<code value="birdsuite-files"/>
<display value="Birdsuite-Files"/>
</concept>
<concept>
<code value="broadpeak"/>
<display value="broadPeak"/>
</concept>
<concept>
<code value="cbs"/>
<display value="CBS"/>
</concept>
<concept>
<code value="chemical-reactivity-probing-profiles"/>
<display value="Chemical-Reactivity-Probing-Profiles"/>
</concept>
<concept>
<code value="chrom-sizes"/>
<display value="chrom-sizes"/>
</concept>
<concept>
<code value="cn"/>
<display value="CN"/>
</concept>
<concept>
<code value="custom-file-formats"/>
<display value="Custom-File-Formats"/>
</concept>
<concept>
<code value="cytoband"/>
<display value="Cytoband"/>
</concept>
<concept>
<code value="fasta"/>
<display value="FASTA"/>
</concept>
<concept>
<code value="gct"/>
<display value="GCT"/>
</concept>
<concept>
<code value="cram"/>
<display value="CRAM"/>
</concept>
<concept>
<code value="genepred"/>
<display value="genePred"/>
</concept>
<concept>
<code value="gff-gtf"/>
<display value="GFF/GTF"/>
</concept>
<concept>
<code value="gistic"/>
<display value="GISTIC"/>
</concept>
<concept>
<code value="goby"/>
<display value="Goby"/>
</concept>
<concept>
<code value="gwas"/>
<display value="GWAS"/>
</concept>
<concept>
<code value="igv"/>
<display value="IGV"/>
</concept>
<concept>
<code value="loh"/>
<display value="LOH"/>
</concept>
<concept>
<code value="maf-multiple-alignment-format"/>
<display value="MAF-Multiple Alignment Format"/>
</concept>
<concept>
<code value="maf-mutation-annotation-format"/>
<display value="MAF-Mutation-Annotation-Format"/>
</concept>
<concept>
<code value="merged-bam-file"/>
<display value="Merged BAM File"/>
</concept>
<concept>
<code value="mut"/>
<display value="MUT"/>
</concept>
<concept>
<code value="narrowpeak"/>
<display value="narrowPeak"/>
</concept>
<concept>
<code value="psl"/>
<display value="PSL"/>
</concept>
<concept>
<code value="res"/>
<display value="RES"/>
</concept>
<concept>
<code value="rna-secondary-structure-formats"/>
<display value="RNA-Secondary-Structure-Formats"/>
</concept>
<concept>
<code value="sam"/>
<display value="SAM"/>
</concept>
<concept>
<code value="sample-info-attributes-file"/>
<display value="Sample-Info-Attributes-file"/>
</concept>
<concept>
<code value="seg"/>
<display value="SEG"/>
</concept>
<concept>
<code value="tdf"/>
<display value="TDF"/>
</concept>
<concept>
<code value="track-line"/>
<display value="Track Line"/>
</concept>
<concept>
<code value="type-line"/>
<display value="Type Line"/>
</concept>
<concept>
<code value="vcf"/>
<display value="VCF"/>
</concept>
<concept>
<code value="wig"/>
<display value="WIG"/>
</concept>
</CodeSystem>