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-ballot 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
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/genomic-study-data-format-vs | Version: 4.0.0-ballot | |||
| Standards status: Trial-use | Maturity Level: 2 | Computable Name: GenomicStudyDataFormatVS | ||
Backport of http://hl7.org/fhir/ValueSet/genomicstudy-dataformat
References
http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs
Expansion performed internally based on codesystem Genomic Study Data Format CodeSystem v4.0.0-ballot (CodeSystem)
This value set contains 40 concepts
| Code | System | Display | Definition |
| bam | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | BAM | BAM |
| bed | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | BED | BED |
| bedpe | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | BEDPE | BEDPE |
| bedgraph | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | BedGraph | BedGraph |
| bigbed | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | bigBed | bigBed |
| bigWig | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | bigWig | bigWig |
| birdsuite-files | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Birdsuite-Files | Birdsuite-Files |
| broadpeak | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | broadPeak | broadPeak |
| cbs | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | CBS | CBS |
| chemical-reactivity-probing-profiles | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Chemical-Reactivity-Probing-Profiles | Chemical-Reactivity-Probing-Profiles |
| chrom-sizes | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | chrom-sizes | chrom-sizes |
| cn | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | CN | CN |
| custom-file-formats | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Custom-File-Formats | Custom-File-Formats |
| cytoband | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Cytoband | Cytoband |
| fasta | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | FASTA | FASTA |
| gct | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | GCT | GCT |
| cram | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | CRAM | CRAM |
| genepred | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | genePred | genePred |
| gff-gtf | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | GFF/GTF | GFF/GTF |
| gistic | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | GISTIC | GISTIC |
| goby | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Goby | Goby |
| gwas | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | GWAS | GWAS |
| igv | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | IGV | IGV |
| loh | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | LOH | LOH |
| maf-multiple-alignment-format | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | MAF-Multiple Alignment Format | MAF-Multiple Alignment Format |
| maf-mutation-annotation-format | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | MAF-Mutation-Annotation-Format | MAF-Mutation-Annotation-Format |
| merged-bam-file | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Merged BAM File | Merged BAM File |
| mut | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | MUT | MUT |
| narrowpeak | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | narrowPeak | narrowPeak |
| psl | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | PSL | PSL |
| res | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | RES | RES |
| rna-secondary-structure-formats | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | RNA-Secondary-Structure-Formats | RNA-Secondary-Structure-Formats |
| sam | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | SAM | SAM |
| sample-info-attributes-file | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Sample-Info-Attributes-file | Sample-Info-Attributes-file |
| seg | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | SEG | SEG |
| tdf | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | TDF | TDF |
| track-line | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Track Line | Track Line |
| type-line | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | Type Line | Type Line |
| vcf | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | VCF | VCF |
| wig | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genomic-study-data-format-cs | WIG | WIG |
Explanation of the columns that may appear on this page:
| Level | A few code lists that FHIR defines are hierarchical - each code is assigned a level. In this scheme, some codes are under other codes, and imply that the code they are under also applies |
| System | The source of the definition of the code (when the value set draws in codes defined elsewhere) |
| Code | The code (used as the code in the resource instance) |
| Display | The display (used in the display element of a Coding). If there is no display, implementers should not simply display the code, but map the concept into their application |
| Definition | An explanation of the meaning of the concept |
| Comments | Additional notes about how to use the code |