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. #GENEIOUS TUTORIAL POINT MUTATION STUDY BAM FILE PDF#
fa-file-text Download PDF /Data/PDF/Data_UG.pdf.Bioinformatics Pipeline: Protein Expression.Bioinformatics Pipeline: Methylation Liftover 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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