The affected codons with the variant base in upper case Relative position of the affected amino acid in proteinĬhange in amino acids (only given if the variant affects the protein-coding sequence) Relative position of base pair in coding sequence Relative position of base pair in cDNA sequence The type of transcript or regulatory feature (e.g. Currently one of Transcript, RegulatoryFeature, MotifFeature. The impact modifier for the consequence type The variant allele used to calculate the consequence VEP Documentation provides additional information about some of these fields. Please refer to the DNA-Seq Analysis Pipeline documentation for details on how this information is generated. The following variant annotation fields are currently included in Annotated Somatic Mutation VCF files. See Variant Call Format (VCF) Version 4.1 Specification for details. TUMOR: Colon-separated values that describe the tumor sample.NORMAL: Colon-separated values that describe the normal sample.This includes descriptions of the colon-separated values. FORMAT: The format of the sample genotype data in the next two columns.This includes the annotation applied by the VEP. INFO: Additional information about the variant.The types of filters used will depend on the variant caller used. FILTER: The names of the filters that have flagged this variant.ALT: The alternate allele(s), comma-separated if there are more than one.REF: The base(s) exhibited by the reference genome at the variant's position.ID: A unique identifier for the variant usually a dbSNP rs number if applicable.Refers to the first position if the variant includes more than one base POS: The position of the variant on the chromosome.CHROM: The chromosome on which the variant is located.VEP: the VEP command used by the Somatic Annotation Workflow to generate the annotated VCF file.Įach variant is represented by a row in the VCF file.Unplaced, unlocalized, human decoy, and viral genome sequences are not included. NOTE: Annotated VCFs include contig information for autosomes, sex chromosomes, and mitochondrial DNA.contig: A list of IDs for the contiguous DNA sequences that appear in the reference genome used to produce VCF files.reference: The reference genome used to generate the VCF file (GRCh38.d1.vd1.fa).FILTER: Description of filters that have been applied to the variants.The last INFO line contains information about annotation fields generated by the Somatic Annotation Workflow (see GDC INFO Fields below). NOTE: GDC Annotated VCFs may contain multiple INFO lines.INFO: Format of additional information fields.BAM_ID: The UUID for the BAM file used to produce the VCF.NAME: Submitter ID (barcode) of the aliquot.NAME: Submitter ID (barcode) associated with the participant.INDIVIDUAL: information about the study participant ( case), including:.Annotated VCF files contain two gdcWorkflow lines, one that reports the variant calling process and one that reports the variant annotation process. gdcWorkflow: Information on the pipelines that were used by the GDC to generate the VCF file.Some key components of this section include: VCF file structure Metadata headerĪ VCF file starts with lines of metadata that begin with #. Raw Simple Somatic Mutation VCF files are unannotated, whereas Annotated Somatic Mutation VCF files include extensive, consistent, and pipeline-agnostic annotation of somatic variants. The GDC VCF file format follows standards of the Variant Call Format (VCF) Version 4.1 Specification. Four additional annotated VCFs (Data Type: Annotated Somatic Mutation) are produced by adding biologically relevant information about each variant. Four raw VCFs (Data Type: Raw Simple Somatic Mutation) are produced for each tumor/normal pair of BAMs. VCF files report the somatic variants that were detected by each of the four variant callers. The GDC DNA-Seq somatic variant-calling pipeline compares a set of matched tumor/normal alignments and produces a VCF file. fa-file-text Download PDF /Data/PDF/Data_UG.pdf.Bioinformatics Pipeline: Protein Expression.Bioinformatics Pipeline: Methylation Analysis Pipeline.Bioinformatics Pipeline: Copy Number Variation Analysis.Bioinformatics Pipeline: miRNA Analysis.Bioinformatics Pipeline: DNA-Seq Analysis.fa-file-text Download PDF /Data_Transfer_Tool/PDF/Data_Transfer_Tool_UG.pdf.Data Transfer Tool Command Line Documentation.fa-file-text Download PDF /Data_Submission_Portal/PDF/Data_Submission_Portal_UG.pdf.Before Submitting Data to the GDC Portal.fa-file-text Download PDF /Data_Portal/PDF/Data_Portal_UG.pdf.fa-file-text Download PDF /API/PDF/API_UG.pdf.Appendix C: Format of Submission Queries and Responses.
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