![.bam file format sequencing data .bam file format sequencing data](http://www.arrayserver.com/wiki/images/8/8e/Ngs_MergeFiles_Menu.png)
For tumor samples that contain variants from multiple combinations of tumor-normal aliquot pairs, only one pair is selected in the Somatic MAF based on their sample type. Somatic MAFs (*somatic.maf), which are also known as Masked Somatic Mutation files, are further processed to remove lower quality and potential germline variants. MAFs are produced by aggregating the GDC annotated VCF files generated from one pipeline for one project.Īnnotated VCF files often have variants reported on multiple transcripts whereas the MAF files generated from the VCFs (*protected.maf) only report the most critically affected one. One MAF file is produced per variant calling pipeline per GDC project. The GDC produces MAF files at two permission levels: protected and somatic (or open-access). MAF files are produced through the Somatic Aggregation Workflow. Mutation Annotation Format (MAF) is a tab-delimited text file with aggregated mutation information from VCF Files and are generated on a project-level.
#.bam file format sequencing data pdf#
![.bam file format sequencing data .bam file format sequencing data](https://i1.rgstatic.net/publication/221803294_Hadoop-BAM_Directly_manipulating_next_generation_sequencing_data_in_the_cloud/links/0deec5178bd5cecd09000000/largepreview.png)
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.
![.bam file format sequencing data .bam file format sequencing data](https://media.springernature.com/full/springer-static/image/art:10.1186%2F1471-2105-13-S7-S12/MediaObjects/12859_2012_Article_5165_Fig5_HTML.jpg)
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.