Clinical Genomics Resource Incubator
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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

ValueSet: Genomic Study Data Format VS (Experimental)

Official URL: http://hl7.org/fhir/uv/cg-incubator/ValueSet/genomicstudy-dataformat Version: 0.1.0-ci-build
Standards status: Draft Draft as of 2022-08-17 Maturity Level: 1 Computable Name: GenomicStudyDataFormatVS
Other Identifiers: OID:2.16.840.1.113883.4.642.3.3084

The data formats relevant to Genomic Study analysis.

References

Logical Definition (CLD)

Last updated: 2020-12-28 16:55:11+1100

Profile: Shareable ValueSet

 

Expansion

Expansion performed internally based on codesystem Genomic Study Data Format v0.1.0-ci-build (CodeSystem)

This value set contains 40 concepts

SystemCodeDisplay (en)DefinitionJSONXML
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  bamBAMBinary Alignment/Map format for storing read alignments against reference sequences.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  bedBEDBrowser Extensible Data format for representing genomic regions and associated annotations.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  bedpeBEDPEPaired-End BED format for representing pairwise genomic interactions.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  bedgraphBedGraphBED Graph format for representing genomic signals as continuous-valued data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  bigbedbigBedBinary indexed BED format for efficiently storing large amounts of genomic region data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  bigWigbigWigBinary indexed Wig format for efficiently storing large amounts of continuous-valued genomic data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  birdsuite-filesBirdsuite-FilesFile format used by the Birdsuite suite of software for SNP genotyping and copy number analysis.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  broadpeakbroadPeakBED format variant for representing broad peaks in ChIP-Seq data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  cbsCBSCopy number data format output by Circular Binary Segmentation analysis.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  chemical-reactivity-probing-profilesChemical-Reactivity-Probing-ProfilesProfiles of chemical reactivity for RNA structure analysis.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  chrom-sizeschrom-sizesFile listing chromosome names and their sizes.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  cnCNCopy number data format.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  custom-file-formatsCustom-File-FormatsUser-defined or proprietary file formats for genomic data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  cytobandCytobandChromosome cytogenetic band locations and characteristics.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  fastaFASTAFormat for representing sequences of nucleic acids or proteins using single letter codes.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  gctGCTGene Cluster Text format for storing gene expression data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  cramCRAMCompressed Reference-Aligned Map format for storing read alignments more compactly than BAM.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  genepredgenePredFormat for storing gene predictions with exon and CDS information.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  gff-gtfGFF/GTFGeneral Feature Format / Gene Transfer Format for storing genomic features and annotations.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  gisticGISTICGenomic Identification of Significant Targets in Cancer output format for copy number analysis.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  gobyGobyCompact file format for storing read alignments, variations, and base quality information.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  gwasGWASGenome-Wide Association Study format for storing association results.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  igvIGVIntegrative Genomics Viewer session or display format.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  lohLOHLoss of Heterozygosity data format.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  maf-multiple-alignment-formatMAF-Multiple Alignment FormatMultiple Alignment Format for storing aligned sequences.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  maf-mutation-annotation-formatMAF-Mutation-Annotation-FormatMutation Annotation Format for storing somatic mutation data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  merged-bam-fileMerged BAM FileBAM file containing read alignments from multiple samples or lanes merged together.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  mutMUTMutation data format.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  narrowpeaknarrowPeakBED format variant for representing narrow peaks in ChIP-Seq data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  pslPSLPattern Space Layout format for storing sequence alignments.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  resRESResolution data format.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  rna-secondary-structure-formatsRNA-Secondary-Structure-FormatsFormats for representing RNA secondary structure information.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  samSAMSequence Alignment/Map format for storing read alignments, the uncompressed version of BAM.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  sample-info-attributes-fileSample-Info-Attributes-fileFile containing sample information and attributes.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  segSEGSegmented data format for storing copy number or other segmented genomic data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  tdfTDFTiled Data Format for efficient storage and display of large genomic datasets.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  track-lineTrack LineUCSC Genome Browser track line header defining display properties for genomic data.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  type-lineType LineType line header for defining genomic data track properties.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  vcfVCFVariant Call Format for storing variant information including SNPs, indels, and structural variations.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/genomicstudy-dataformat  wigWIGWiggle Track format for storing continuous-valued genomic data.

Description of the above table(s).