Cqgc Implementation Guide
0.1.0 - CI Build
Cqgc Implementation Guide - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
| Active as of 2025-08-25 |
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<id value="data-type"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem data-type</b></p><a name="data-type"> </a><a name="hcdata-type"> </a><p>This case-sensitive code system <code>http://fhir.cqgc.ferlab.bio/CodeSystem/data-type</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>French (fr)</b></td></tr><tr><td style="white-space:nowrap">ALIR<a name="data-type-ALIR"> </a></td><td>Aligned Reads</td><td>Fragments alignés</td></tr><tr><td style="white-space:nowrap">ALIRPG<a name="data-type-ALIRPG"> </a></td><td>Aligned Reads from Variants Non-Repetitive Regions Report</td><td>Fragments alignés pour les variants annotés provenant de régions non répétées</td></tr><tr><td style="white-space:nowrap">SNV<a name="data-type-SNV"> </a></td><td>Germline SNV</td><td>SNV germinal</td></tr><tr><td style="white-space:nowrap">SSNV<a name="data-type-SSNV"> </a></td><td>Somatic SNV</td><td>SNV somatic</td></tr><tr><td style="white-space:nowrap">SNVPG<a name="data-type-SNVPG"> </a></td><td>Germline SNV from Variants Non-Repetitive Regions Report</td><td>Variants SNV germinales annotés provenant de régions non répétées</td></tr><tr><td style="white-space:nowrap">GCNV<a name="data-type-GCNV"> </a></td><td>Germline CNV</td><td>CNV germinal</td></tr><tr><td style="white-space:nowrap">SCNV<a name="data-type-SCNV"> </a></td><td>Somatic CNV</td><td>CNV somatic</td></tr><tr><td style="white-space:nowrap">GSV<a name="data-type-GSV"> </a></td><td>Germline SV</td><td>SV germinal</td></tr><tr><td style="white-space:nowrap">SSV<a name="data-type-SSV"> </a></td><td>Somatic SV</td><td>SV somatic</td></tr><tr><td style="white-space:nowrap">SOMFU<a name="data-type-SOMFU"> </a></td><td>Somatic Fusion Dragen VCF</td><td>VCF Dragen des fusions somatiques</td></tr><tr><td style="white-space:nowrap">SSUP<a name="data-type-SSUP"> </a></td><td>Sequencing Data Supplement</td><td>Données de séquençage supplémentaires</td></tr><tr><td style="white-space:nowrap">IGV<a name="data-type-IGV"> </a></td><td>IGV Track</td><td>Track IGV</td></tr><tr><td style="white-space:nowrap">CNVVIS<a name="data-type-CNVVIS"> </a></td><td>CNV Visualization</td><td>Visualization de CNVs</td></tr><tr><td style="white-space:nowrap">EXP<a name="data-type-EXP"> </a></td><td>Expression PNG</td><td>PNG des expressions</td></tr><tr><td style="white-space:nowrap">COVGENE<a name="data-type-COVGENE"> </a></td><td>Coverage by Gene Report</td><td>Rapport de couverture par gène</td></tr><tr><td style="white-space:nowrap">QCRUN<a name="data-type-QCRUN"> </a></td><td>Sequencing Run QC Report</td><td>Rapport de controle de qualité de la run de séquençage</td></tr><tr><td style="white-space:nowrap">EXOMISER<a name="data-type-EXOMISER"> </a></td><td>Exomiser SNV Report</td><td>Rapport SNV Exomiser</td></tr><tr><td style="white-space:nowrap">EXOMISER_CNV<a name="data-type-EXOMISER_CNV"> </a></td><td>Exomiser CNV Report</td><td>Rapport CNV Exomiser</td></tr><tr><td style="white-space:nowrap">PFUSION<a name="data-type-PFUSION"> </a></td><td>Preliminary Fusion TSV</td><td>TSV préliminaire des fusions</td></tr><tr><td style="white-space:nowrap">RNASEQ<a name="data-type-RNASEQ"> </a></td><td>RNA Sequences</td><td>Séquences d'ARN</td></tr><tr><td style="white-space:nowrap">SRNASEQFCP<a name="data-type-SRNASEQFCP"> </a></td><td>Somatic RNA Sequences Fusion Candidate Preliminary</td><td>Fichier préliminaire des candidats de fusion de séquences d'ARN somatique</td></tr><tr><td style="white-space:nowrap">SRNASEQFCF<a name="data-type-SRNASEQFCF"> </a></td><td>Somatic RNA Sequences Fusion Candidate Final</td><td>Fichier final des candidats de fusion de séquences d'ARN somatique</td></tr><tr><td style="white-space:nowrap">SGENEXPSF<a name="data-type-SGENEXPSF"> </a></td><td>Somatic Gene Expression SF</td><td>Expression génique somatique SF</td></tr><tr><td style="white-space:nowrap">FFUSION<a name="data-type-FFUSION"> </a></td><td>Final Fusion</td><td>Final des fusions</td></tr><tr><td style="white-space:nowrap">MDALL<a name="data-type-MDALL"> </a></td><td>Leukemia Classification by the MD-ALL Algorithm</td><td>Classification de la leucémie par l'algorithme MD-ALL</td></tr><tr><td style="white-space:nowrap">KMBCOR<a name="data-type-KMBCOR"> </a></td><td>Somatic Targeted Analysis by the KM Algorithm</td><td>Analyse ciblée somatique par l'algorithme KM</td></tr><tr><td style="white-space:nowrap">KMFLT3<a name="data-type-KMFLT3"> </a></td><td>Somatic Targeted Analysis by the KM Algorithm</td><td>Analyse ciblée somatique par l'algorithme KM</td></tr><tr><td style="white-space:nowrap">KMUBTF<a name="data-type-KMUBTF"> </a></td><td>Somatic Targeted Analysis by the KM Algorithm</td><td>Analyse ciblée somatique par l'algorithme KM</td></tr><tr><td style="white-space:nowrap">KMNPM1<a name="data-type-KMNPM1"> </a></td><td>Somatic Targeted Analysis by the KM Algorithm</td><td>Analyse ciblée somatique par l'algorithme KM</td></tr><tr><td style="white-space:nowrap">INDX<a name="data-type-INDX"> </a></td><td>Sequencing Data Index</td><td>Index de données de séquençage</td></tr><tr><td style="white-space:nowrap">OTHER<a name="data-type-OTHER"> </a></td><td>Undefined Data Type</td><td>Type de données indéfini</td></tr><tr><td style="white-space:nowrap">FUSG<a name="data-type-FUSG"> </a></td><td>Gene fusion</td><td>Fusion de gènes</td></tr><tr><td style="white-space:nowrap">HLA<a name="data-type-HLA"> </a></td><td>HLA Caller Results</td><td>Résultats de l'appel des allèles HLA</td></tr><tr><td style="white-space:nowrap">PAC<a name="data-type-PAC"> </a></td><td>Paralog Calling</td><td>Appel de variants dans les gènes paralogues</td></tr><tr><td style="white-space:nowrap">PEC<a name="data-type-PEC"> </a></td><td>Ploidy Estimation per Chromosome</td><td>Estimation de la ploïdie par chromosome</td></tr><tr><td style="white-space:nowrap">ROH<a name="data-type-ROH"> </a></td><td>Runs of Homozygosity</td><td>Segments d’homozygotie</td></tr><tr><td style="white-space:nowrap">STR<a name="data-type-STR"> </a></td><td>Tandem Repeat Calls</td><td>Appel de répétions en tandem</td></tr><tr><td style="white-space:nowrap">NORM_VEPPG<a name="data-type-NORM_VEPPG"> </a></td><td>Annotated Variants from Non-Repetitive Regions (Legacy Batch) VCF File</td><td>Fichier VCF des variants annotés provenant de régions non répétées (ancien traitement par lot)</td></tr><tr><td style="white-space:nowrap">NRRV<a name="data-type-NRRV"> </a></td><td>Annotated Variants from Non-Repetitive Regions Report</td><td>Rapport de variants annotés provenant de régions non répétées</td></tr><tr><td style="white-space:nowrap">PHENOVAR<a name="data-type-PHENOVAR"> </a></td><td>Phenovar Detailed Results</td><td>Résultats détaillés de Phenovar</td></tr></table></div>
</text>
<url value="http://fhir.cqgc.ferlab.bio/CodeSystem/data-type"/>
<version value="0.1.0"/>
<name value="data-type"/>
<title value="Data types"/>
<status value="active"/>
<experimental value="false"/>
<date value="2025-08-25T15:12:45+00:00"/>
<publisher value="Ferlab.bio"/>
<contact>
<name value="Cqgc"/>
<telecom>
<system value="email"/>
<value value="mailto:support@ferlab.bio"/>
</telecom>
</contact>
<description value="Data types"/>
<caseSensitive value="true"/>
<content value="complete"/>
<count value="5"/>
<concept>
<code value="ALIR"/>
<display value="Aligned Reads"/>
<designation>
<language value="fr"/>
<value value="Fragments alignés"/>
</designation>
</concept>
<concept>
<code value="ALIRPG"/>
<display
value="Aligned Reads from Variants Non-Repetitive Regions Report"/>
<designation>
<language value="fr"/>
<value
value="Fragments alignés pour les variants annotés provenant de régions non répétées"/>
</designation>
</concept>
<concept>
<code value="SNV"/>
<display value="Germline SNV"/>
<designation>
<language value="fr"/>
<value value="SNV germinal"/>
</designation>
</concept>
<concept>
<code value="SSNV"/>
<display value="Somatic SNV"/>
<designation>
<language value="fr"/>
<value value="SNV somatic"/>
</designation>
</concept>
<concept>
<code value="SNVPG"/>
<display
value="Germline SNV from Variants Non-Repetitive Regions Report"/>
<designation>
<language value="fr"/>
<value
value="Variants SNV germinales annotés provenant de régions non répétées"/>
</designation>
</concept>
<concept>
<code value="GCNV"/>
<display value="Germline CNV"/>
<designation>
<language value="fr"/>
<value value="CNV germinal"/>
</designation>
</concept>
<concept>
<code value="SCNV"/>
<display value="Somatic CNV"/>
<designation>
<language value="fr"/>
<value value="CNV somatic"/>
</designation>
</concept>
<concept>
<code value="GSV"/>
<display value="Germline SV"/>
<designation>
<language value="fr"/>
<value value="SV germinal"/>
</designation>
</concept>
<concept>
<code value="SSV"/>
<display value="Somatic SV"/>
<designation>
<language value="fr"/>
<value value="SV somatic"/>
</designation>
</concept>
<concept>
<code value="SOMFU"/>
<display value="Somatic Fusion Dragen VCF"/>
<designation>
<language value="fr"/>
<value value="VCF Dragen des fusions somatiques"/>
</designation>
</concept>
<concept>
<code value="SSUP"/>
<display value="Sequencing Data Supplement"/>
<designation>
<language value="fr"/>
<value value="Données de séquençage supplémentaires"/>
</designation>
</concept>
<concept>
<code value="IGV"/>
<display value="IGV Track"/>
<designation>
<language value="fr"/>
<value value="Track IGV"/>
</designation>
</concept>
<concept>
<code value="CNVVIS"/>
<display value="CNV Visualization"/>
<designation>
<language value="fr"/>
<value value="Visualization de CNVs"/>
</designation>
</concept>
<concept>
<code value="EXP"/>
<display value="Expression PNG"/>
<designation>
<language value="fr"/>
<value value="PNG des expressions"/>
</designation>
</concept>
<concept>
<code value="COVGENE"/>
<display value="Coverage by Gene Report"/>
<designation>
<language value="fr"/>
<value value="Rapport de couverture par gène"/>
</designation>
</concept>
<concept>
<code value="QCRUN"/>
<display value="Sequencing Run QC Report"/>
<designation>
<language value="fr"/>
<value value="Rapport de controle de qualité de la run de séquençage"/>
</designation>
</concept>
<concept>
<code value="EXOMISER"/>
<display value="Exomiser SNV Report"/>
<designation>
<language value="fr"/>
<value value="Rapport SNV Exomiser"/>
</designation>
</concept>
<concept>
<code value="EXOMISER_CNV"/>
<display value="Exomiser CNV Report"/>
<designation>
<language value="fr"/>
<value value="Rapport CNV Exomiser"/>
</designation>
</concept>
<concept>
<code value="PFUSION"/>
<display value="Preliminary Fusion TSV"/>
<designation>
<language value="fr"/>
<value value="TSV préliminaire des fusions"/>
</designation>
</concept>
<concept>
<code value="RNASEQ"/>
<display value="RNA Sequences"/>
<designation>
<language value="fr"/>
<value value="Séquences d'ARN"/>
</designation>
</concept>
<concept>
<code value="SRNASEQFCP"/>
<display value="Somatic RNA Sequences Fusion Candidate Preliminary"/>
<designation>
<language value="fr"/>
<value
value="Fichier préliminaire des candidats de fusion de séquences d'ARN somatique"/>
</designation>
</concept>
<concept>
<code value="SRNASEQFCF"/>
<display value="Somatic RNA Sequences Fusion Candidate Final"/>
<designation>
<language value="fr"/>
<value
value="Fichier final des candidats de fusion de séquences d'ARN somatique"/>
</designation>
</concept>
<concept>
<code value="SGENEXPSF"/>
<display value="Somatic Gene Expression SF"/>
<designation>
<language value="fr"/>
<value value="Expression génique somatique SF"/>
</designation>
</concept>
<concept>
<code value="FFUSION"/>
<display value="Final Fusion"/>
<designation>
<language value="fr"/>
<value value="Final des fusions"/>
</designation>
</concept>
<concept>
<code value="MDALL"/>
<display value="Leukemia Classification by the MD-ALL Algorithm"/>
<designation>
<language value="fr"/>
<value value="Classification de la leucémie par l'algorithme MD-ALL"/>
</designation>
</concept>
<concept>
<code value="KMBCOR"/>
<display value="Somatic Targeted Analysis by the KM Algorithm"/>
<designation>
<language value="fr"/>
<value value="Analyse ciblée somatique par l'algorithme KM"/>
</designation>
</concept>
<concept>
<code value="KMFLT3"/>
<display value="Somatic Targeted Analysis by the KM Algorithm"/>
<designation>
<language value="fr"/>
<value value="Analyse ciblée somatique par l'algorithme KM"/>
</designation>
</concept>
<concept>
<code value="KMUBTF"/>
<display value="Somatic Targeted Analysis by the KM Algorithm"/>
<designation>
<language value="fr"/>
<value value="Analyse ciblée somatique par l'algorithme KM"/>
</designation>
</concept>
<concept>
<code value="KMNPM1"/>
<display value="Somatic Targeted Analysis by the KM Algorithm"/>
<designation>
<language value="fr"/>
<value value="Analyse ciblée somatique par l'algorithme KM"/>
</designation>
</concept>
<concept>
<code value="INDX"/>
<display value="Sequencing Data Index"/>
<designation>
<language value="fr"/>
<value value="Index de données de séquençage"/>
</designation>
</concept>
<concept>
<code value="OTHER"/>
<display value="Undefined Data Type"/>
<designation>
<language value="fr"/>
<value value="Type de données indéfini"/>
</designation>
</concept>
<concept>
<code value="FUSG"/>
<display value="Gene fusion"/>
<designation>
<language value="fr"/>
<value value="Fusion de gènes"/>
</designation>
</concept>
<concept>
<code value="HLA"/>
<display value="HLA Caller Results"/>
<designation>
<language value="fr"/>
<value value="Résultats de l'appel des allèles HLA"/>
</designation>
</concept>
<concept>
<code value="PAC"/>
<display value="Paralog Calling"/>
<designation>
<language value="fr"/>
<value value="Appel de variants dans les gènes paralogues"/>
</designation>
</concept>
<concept>
<code value="PEC"/>
<display value="Ploidy Estimation per Chromosome"/>
<designation>
<language value="fr"/>
<value value="Estimation de la ploïdie par chromosome"/>
</designation>
</concept>
<concept>
<code value="ROH"/>
<display value="Runs of Homozygosity"/>
<designation>
<language value="fr"/>
<value value="Segments d’homozygotie"/>
</designation>
</concept>
<concept>
<code value="STR"/>
<display value="Tandem Repeat Calls"/>
<designation>
<language value="fr"/>
<value value="Appel de répétions en tandem"/>
</designation>
</concept>
<concept>
<code value="NORM_VEPPG"/>
<display
value="Annotated Variants from Non-Repetitive Regions (Legacy Batch) VCF File"/>
<designation>
<language value="fr"/>
<value
value="Fichier VCF des variants annotés provenant de régions non répétées (ancien traitement par lot)"/>
</designation>
</concept>
<concept>
<code value="NRRV"/>
<display value="Annotated Variants from Non-Repetitive Regions Report"/>
<designation>
<language value="fr"/>
<value
value="Rapport de variants annotés provenant de régions non répétées"/>
</designation>
</concept>
<concept>
<code value="PHENOVAR"/>
<display value="Phenovar Detailed Results"/>
<designation>
<language value="fr"/>
<value value="Résultats détaillés de Phenovar"/>
</designation>
</concept>
</CodeSystem>