Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build
Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
| Page standards status: Draft | Maturity Level: 1 |
<CodeSystem xmlns="http://hl7.org/fhir">
<id value="genomicstudy-dataformat"/>
<meta>
<lastUpdated value="2021-01-05T10:01:24.148+11:00"/>
<profile
value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/>
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<language value="en"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem genomicstudy-dataformat</b></p><a name="genomicstudy-dataformat"> </a><a name="hcgenomicstudy-dataformat"> </a><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Last updated: 2021-01-05 10:01:24+1100</p><p style="margin-bottom: 0px">Profile: <a href="http://hl7.org/fhir/R5/shareablecodesystem.html">Shareable CodeSystem</a></p></div><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat</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="genomicstudy-dataformat-bam"> </a></td><td>BAM</td><td>Binary Alignment/Map format for storing read alignments against reference sequences.</td></tr><tr><td style="white-space:nowrap">bed<a name="genomicstudy-dataformat-bed"> </a></td><td>BED</td><td>Browser Extensible Data format for representing genomic regions and associated annotations.</td></tr><tr><td style="white-space:nowrap">bedpe<a name="genomicstudy-dataformat-bedpe"> </a></td><td>BEDPE</td><td>Paired-End BED format for representing pairwise genomic interactions.</td></tr><tr><td style="white-space:nowrap">bedgraph<a name="genomicstudy-dataformat-bedgraph"> </a></td><td>BedGraph</td><td>BED Graph format for representing genomic signals as continuous-valued data.</td></tr><tr><td style="white-space:nowrap">bigbed<a name="genomicstudy-dataformat-bigbed"> </a></td><td>bigBed</td><td>Binary indexed BED format for efficiently storing large amounts of genomic region data.</td></tr><tr><td style="white-space:nowrap">bigWig<a name="genomicstudy-dataformat-bigWig"> </a></td><td>bigWig</td><td>Binary indexed Wig format for efficiently storing large amounts of continuous-valued genomic data.</td></tr><tr><td style="white-space:nowrap">birdsuite-files<a name="genomicstudy-dataformat-birdsuite-files"> </a></td><td>Birdsuite-Files</td><td>File format used by the Birdsuite suite of software for SNP genotyping and copy number analysis.</td></tr><tr><td style="white-space:nowrap">broadpeak<a name="genomicstudy-dataformat-broadpeak"> </a></td><td>broadPeak</td><td>BED format variant for representing broad peaks in ChIP-Seq data.</td></tr><tr><td style="white-space:nowrap">cbs<a name="genomicstudy-dataformat-cbs"> </a></td><td>CBS</td><td>Copy number data format output by Circular Binary Segmentation analysis.</td></tr><tr><td style="white-space:nowrap">chemical-reactivity-probing-profiles<a name="genomicstudy-dataformat-chemical-reactivity-probing-profiles"> </a></td><td>Chemical-Reactivity-Probing-Profiles</td><td>Profiles of chemical reactivity for RNA structure analysis.</td></tr><tr><td style="white-space:nowrap">chrom-sizes<a name="genomicstudy-dataformat-chrom-sizes"> </a></td><td>chrom-sizes</td><td>File listing chromosome names and their sizes.</td></tr><tr><td style="white-space:nowrap">cn<a name="genomicstudy-dataformat-cn"> </a></td><td>CN</td><td>Copy number data format.</td></tr><tr><td style="white-space:nowrap">custom-file-formats<a name="genomicstudy-dataformat-custom-file-formats"> </a></td><td>Custom-File-Formats</td><td>User-defined or proprietary file formats for genomic data.</td></tr><tr><td style="white-space:nowrap">cytoband<a name="genomicstudy-dataformat-cytoband"> </a></td><td>Cytoband</td><td>Chromosome cytogenetic band locations and characteristics.</td></tr><tr><td style="white-space:nowrap">fasta<a name="genomicstudy-dataformat-fasta"> </a></td><td>FASTA</td><td>Format for representing sequences of nucleic acids or proteins using single letter codes.</td></tr><tr><td style="white-space:nowrap">gct<a name="genomicstudy-dataformat-gct"> </a></td><td>GCT</td><td>Gene Cluster Text format for storing gene expression data.</td></tr><tr><td style="white-space:nowrap">cram<a name="genomicstudy-dataformat-cram"> </a></td><td>CRAM</td><td>Compressed Reference-Aligned Map format for storing read alignments more compactly than BAM.</td></tr><tr><td style="white-space:nowrap">genepred<a name="genomicstudy-dataformat-genepred"> </a></td><td>genePred</td><td>Format for storing gene predictions with exon and CDS information.</td></tr><tr><td style="white-space:nowrap">gff-gtf<a name="genomicstudy-dataformat-gff-gtf"> </a></td><td>GFF/GTF</td><td>General Feature Format / Gene Transfer Format for storing genomic features and annotations.</td></tr><tr><td style="white-space:nowrap">gistic<a name="genomicstudy-dataformat-gistic"> </a></td><td>GISTIC</td><td>Genomic Identification of Significant Targets in Cancer output format for copy number analysis.</td></tr><tr><td style="white-space:nowrap">goby<a name="genomicstudy-dataformat-goby"> </a></td><td>Goby</td><td>Compact file format for storing read alignments, variations, and base quality information.</td></tr><tr><td style="white-space:nowrap">gwas<a name="genomicstudy-dataformat-gwas"> </a></td><td>GWAS</td><td>Genome-Wide Association Study format for storing association results.</td></tr><tr><td style="white-space:nowrap">igv<a name="genomicstudy-dataformat-igv"> </a></td><td>IGV</td><td>Integrative Genomics Viewer session or display format.</td></tr><tr><td style="white-space:nowrap">loh<a name="genomicstudy-dataformat-loh"> </a></td><td>LOH</td><td>Loss of Heterozygosity data format.</td></tr><tr><td style="white-space:nowrap">maf-multiple-alignment-format<a name="genomicstudy-dataformat-maf-multiple-alignment-format"> </a></td><td>MAF-Multiple Alignment Format</td><td>Multiple Alignment Format for storing aligned sequences.</td></tr><tr><td style="white-space:nowrap">maf-mutation-annotation-format<a name="genomicstudy-dataformat-maf-mutation-annotation-format"> </a></td><td>MAF-Mutation-Annotation-Format</td><td>Mutation Annotation Format for storing somatic mutation data.</td></tr><tr><td style="white-space:nowrap">merged-bam-file<a name="genomicstudy-dataformat-merged-bam-file"> </a></td><td>Merged BAM File</td><td>BAM file containing read alignments from multiple samples or lanes merged together.</td></tr><tr><td style="white-space:nowrap">mut<a name="genomicstudy-dataformat-mut"> </a></td><td>MUT</td><td>Mutation data format.</td></tr><tr><td style="white-space:nowrap">narrowpeak<a name="genomicstudy-dataformat-narrowpeak"> </a></td><td>narrowPeak</td><td>BED format variant for representing narrow peaks in ChIP-Seq data.</td></tr><tr><td style="white-space:nowrap">psl<a name="genomicstudy-dataformat-psl"> </a></td><td>PSL</td><td>Pattern Space Layout format for storing sequence alignments.</td></tr><tr><td style="white-space:nowrap">res<a name="genomicstudy-dataformat-res"> </a></td><td>RES</td><td>Resolution data format.</td></tr><tr><td style="white-space:nowrap">rna-secondary-structure-formats<a name="genomicstudy-dataformat-rna-secondary-structure-formats"> </a></td><td>RNA-Secondary-Structure-Formats</td><td>Formats for representing RNA secondary structure information.</td></tr><tr><td style="white-space:nowrap">sam<a name="genomicstudy-dataformat-sam"> </a></td><td>SAM</td><td>Sequence Alignment/Map format for storing read alignments, the uncompressed version of BAM.</td></tr><tr><td style="white-space:nowrap">sample-info-attributes-file<a name="genomicstudy-dataformat-sample-info-attributes-file"> </a></td><td>Sample-Info-Attributes-file</td><td>File containing sample information and attributes.</td></tr><tr><td style="white-space:nowrap">seg<a name="genomicstudy-dataformat-seg"> </a></td><td>SEG</td><td>Segmented data format for storing copy number or other segmented genomic data.</td></tr><tr><td style="white-space:nowrap">tdf<a name="genomicstudy-dataformat-tdf"> </a></td><td>TDF</td><td>Tiled Data Format for efficient storage and display of large genomic datasets.</td></tr><tr><td style="white-space:nowrap">track-line<a name="genomicstudy-dataformat-track-line"> </a></td><td>Track Line</td><td>UCSC Genome Browser track line header defining display properties for genomic data.</td></tr><tr><td style="white-space:nowrap">type-line<a name="genomicstudy-dataformat-type-line"> </a></td><td>Type Line</td><td>Type line header for defining genomic data track properties.</td></tr><tr><td style="white-space:nowrap">vcf<a name="genomicstudy-dataformat-vcf"> </a></td><td>VCF</td><td>Variant Call Format for storing variant information including SNPs, indels, and structural variations.</td></tr><tr><td style="white-space:nowrap">wig<a name="genomicstudy-dataformat-wig"> </a></td><td>WIG</td><td>Wiggle Track format for storing continuous-valued genomic data.</td></tr></table></div>
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url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
<valueCode value="cg"/>
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<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
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url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
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<url
value="http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat"/>
<identifier>
<system value="urn:ietf:rfc:3986"/>
<value value="urn:oid:2.16.840.1.113883.4.642.4.1978"/>
</identifier>
<version value="0.1.0-ci-build"/>
<name value="GenomicStudyDataFormat"/>
<title value="Genomic Study Data Format"/>
<status value="draft"/>
<experimental value="true"/>
<date value="2022-08-17T14:49:24-05:00"/>
<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="clingenomics@lists.hl7.org"/>
</telecom>
</contact>
<description
value="The data format relevant to genomics. These formats and relevant codes were pulled from [Integrative Genomics Viewer Documentation](https://software.broadinstitute.org/software/igv/FileFormats) by Broad Institute."/>
<jurisdiction>
<coding>
<system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
<code value="001"/>
<display value="World"/>
</coding>
</jurisdiction>
<caseSensitive value="true"/>
<valueSet
value="http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-dataformat"/>
<content value="complete"/>
<concept>
<code value="bam"/>
<display value="BAM"/>
<definition
value="Binary Alignment/Map format for storing read alignments against reference sequences."/>
</concept>
<concept>
<code value="bed"/>
<display value="BED"/>
<definition
value="Browser Extensible Data format for representing genomic regions and associated annotations."/>
</concept>
<concept>
<code value="bedpe"/>
<display value="BEDPE"/>
<definition
value="Paired-End BED format for representing pairwise genomic interactions."/>
</concept>
<concept>
<code value="bedgraph"/>
<display value="BedGraph"/>
<definition
value="BED Graph format for representing genomic signals as continuous-valued data."/>
</concept>
<concept>
<code value="bigbed"/>
<display value="bigBed"/>
<definition
value="Binary indexed BED format for efficiently storing large amounts of genomic region data."/>
</concept>
<concept>
<code value="bigWig"/>
<display value="bigWig"/>
<definition
value="Binary indexed Wig format for efficiently storing large amounts of continuous-valued genomic data."/>
</concept>
<concept>
<code value="birdsuite-files"/>
<display value="Birdsuite-Files"/>
<definition
value="File format used by the Birdsuite suite of software for SNP genotyping and copy number analysis."/>
</concept>
<concept>
<code value="broadpeak"/>
<display value="broadPeak"/>
<definition
value="BED format variant for representing broad peaks in ChIP-Seq data."/>
</concept>
<concept>
<code value="cbs"/>
<display value="CBS"/>
<definition
value="Copy number data format output by Circular Binary Segmentation analysis."/>
</concept>
<concept>
<code value="chemical-reactivity-probing-profiles"/>
<display value="Chemical-Reactivity-Probing-Profiles"/>
<definition
value="Profiles of chemical reactivity for RNA structure analysis."/>
</concept>
<concept>
<code value="chrom-sizes"/>
<display value="chrom-sizes"/>
<definition value="File listing chromosome names and their sizes."/>
</concept>
<concept>
<code value="cn"/>
<display value="CN"/>
<definition value="Copy number data format."/>
</concept>
<concept>
<code value="custom-file-formats"/>
<display value="Custom-File-Formats"/>
<definition
value="User-defined or proprietary file formats for genomic data."/>
</concept>
<concept>
<code value="cytoband"/>
<display value="Cytoband"/>
<definition
value="Chromosome cytogenetic band locations and characteristics."/>
</concept>
<concept>
<code value="fasta"/>
<display value="FASTA"/>
<definition
value="Format for representing sequences of nucleic acids or proteins using single letter codes."/>
</concept>
<concept>
<code value="gct"/>
<display value="GCT"/>
<definition
value="Gene Cluster Text format for storing gene expression data."/>
</concept>
<concept>
<code value="cram"/>
<display value="CRAM"/>
<definition
value="Compressed Reference-Aligned Map format for storing read alignments more compactly than BAM."/>
</concept>
<concept>
<code value="genepred"/>
<display value="genePred"/>
<definition
value="Format for storing gene predictions with exon and CDS information."/>
</concept>
<concept>
<code value="gff-gtf"/>
<display value="GFF/GTF"/>
<definition
value="General Feature Format / Gene Transfer Format for storing genomic features and annotations."/>
</concept>
<concept>
<code value="gistic"/>
<display value="GISTIC"/>
<definition
value="Genomic Identification of Significant Targets in Cancer output format for copy number analysis."/>
</concept>
<concept>
<code value="goby"/>
<display value="Goby"/>
<definition
value="Compact file format for storing read alignments, variations, and base quality information."/>
</concept>
<concept>
<code value="gwas"/>
<display value="GWAS"/>
<definition
value="Genome-Wide Association Study format for storing association results."/>
</concept>
<concept>
<code value="igv"/>
<display value="IGV"/>
<definition
value="Integrative Genomics Viewer session or display format."/>
</concept>
<concept>
<code value="loh"/>
<display value="LOH"/>
<definition value="Loss of Heterozygosity data format."/>
</concept>
<concept>
<code value="maf-multiple-alignment-format"/>
<display value="MAF-Multiple Alignment Format"/>
<definition
value="Multiple Alignment Format for storing aligned sequences."/>
</concept>
<concept>
<code value="maf-mutation-annotation-format"/>
<display value="MAF-Mutation-Annotation-Format"/>
<definition
value="Mutation Annotation Format for storing somatic mutation data."/>
</concept>
<concept>
<code value="merged-bam-file"/>
<display value="Merged BAM File"/>
<definition
value="BAM file containing read alignments from multiple samples or lanes merged together."/>
</concept>
<concept>
<code value="mut"/>
<display value="MUT"/>
<definition value="Mutation data format."/>
</concept>
<concept>
<code value="narrowpeak"/>
<display value="narrowPeak"/>
<definition
value="BED format variant for representing narrow peaks in ChIP-Seq data."/>
</concept>
<concept>
<code value="psl"/>
<display value="PSL"/>
<definition
value="Pattern Space Layout format for storing sequence alignments."/>
</concept>
<concept>
<code value="res"/>
<display value="RES"/>
<definition value="Resolution data format."/>
</concept>
<concept>
<code value="rna-secondary-structure-formats"/>
<display value="RNA-Secondary-Structure-Formats"/>
<definition
value="Formats for representing RNA secondary structure information."/>
</concept>
<concept>
<code value="sam"/>
<display value="SAM"/>
<definition
value="Sequence Alignment/Map format for storing read alignments, the uncompressed version of BAM."/>
</concept>
<concept>
<code value="sample-info-attributes-file"/>
<display value="Sample-Info-Attributes-file"/>
<definition value="File containing sample information and attributes."/>
</concept>
<concept>
<code value="seg"/>
<display value="SEG"/>
<definition
value="Segmented data format for storing copy number or other segmented genomic data."/>
</concept>
<concept>
<code value="tdf"/>
<display value="TDF"/>
<definition
value="Tiled Data Format for efficient storage and display of large genomic datasets."/>
</concept>
<concept>
<code value="track-line"/>
<display value="Track Line"/>
<definition
value="UCSC Genome Browser track line header defining display properties for genomic data."/>
</concept>
<concept>
<code value="type-line"/>
<display value="Type Line"/>
<definition
value="Type line header for defining genomic data track properties."/>
</concept>
<concept>
<code value="vcf"/>
<display value="VCF"/>
<definition
value="Variant Call Format for storing variant information including SNPs, indels, and structural variations."/>
</concept>
<concept>
<code value="wig"/>
<display value="WIG"/>
<definition
value="Wiggle Track format for storing continuous-valued genomic data."/>
</concept>
</CodeSystem>
IG © 2026+ HL7 International / Clinical Genomics.
Package hl7.fhir.uv.cg-incubator#0.1.0-ci-build based on FHIR 6.0.0-ballot3.
Generated
2026-03-24
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