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