 Description	This dataset contains data on masked somatic mutations.<br>
                                    It is directly derived from data available on the Genomic Data Commons portal and transformed into GDM format through the openGDC pipeline.<br>
                                    Documentation is available at http://bioinf.iasi.cnr.it/opengdc/data/OpenGDC_format_definition.pdf.<br>
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                                    This type of Next Generation Sequencing (NGS) experiment discovers mutations by aligning DNA sequences derived from tumor samples to sequences derived from normal samples and a reference sequence. A Mutation Annotation Format (MAF) file is used to specify, for each sample, the discovered putative or validated mutations and to categorize those mutations (SNP, deletion, or insertion) as somatic (originating in the tissue) or germline (originating from the germline), as well as to specify additional information for those mutations.<br>
                                    More details are available at https://docs.gdc.cancer.gov/Data/PDF/Data_UG.pdf and at https://gdc.cancer.gov/about-data/data-harmonization-and-generation/genomic-data-harmonization/high-level-data-generation/dna-seq-somatic-variation <br>
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                                    The dataset includes tab-separated BED files, in which each original DNA-seq .maf file is converted, with the following 18 fields, the main ones in the original MAF file: <br>
                                    <ol>
                                    <li>chrom (i.e., the name of the chromosome, e.g., "chr3", "chrY", "chr2_random", equal to the 5. field of the GDC MAF file)</li>
                                    <li>start (i.e., the starting position of the feature in the chromosome or scaffold, e.g., 999, equal to the 6. field of the GDC MAF file)</li>
                                    <li>end (i.e., the ending position of the feature in the chromosome or scaffold, e.g., 1000, equal to the 7. field of the GDC MAF file)</li>
                                    <li>strand (i.e., the DNA strand where the feature is observed, either '+' or '-', equal to the 8. field of the GDC MAF file)</li>
                                    <li>gene_symbol (i.e., the symbol of the gene related to the reported variant, if it exists, e.g., "HRG", equal to the 1. field of the GDC MAF file)</li>
                                    <li>entrez_gene_id (i.e., the Entrez gene ID of the gene related to the reported variant, if it exists, e.g., "3273", equal to the 2. field of the GDC MAF file)</li>
                                    <li>variant_classification (i.e., the classification of the reported variant, e.g., "Missense_Mutation", equal to the 9. field of the GDC MAF file)</li>
                                    <li>variant_type (i.e., the type of mutation, e.g., "INS", equal to the 10. field of the GDC MAF file)</li>
                                    <li>reference_allele (i.e., the plus strand reference allele at the variant position, e.g., "A", equal to the 11. field of the GDC MAF file)</li>
                                    <li>tumor_seq_allele1 (i.e., the tumor sequencing (discovery) allele 1, e.g., "C", equal to the 12. field of the GDC MAF file)</li>
                                    <li>tumor_seq_allele2 (i.e., the tumor sequencing (discovery) allele 2, e.g., "G", equal to the 13. field of the GDC MAF file)</li>
                                    <li>dbsnp_rs (i.e., the latest dbSNP rs ID, e.g., "rs12345" or "novel" if not present in dbSNP, equal to the 14. field of the GDC MAF file)</li>
                                    <li>tumor_sample_barcode (i.e., the BCR aliquot barcode for the tumor sample, e.g., "TCGA-02-0021-01A-01D-0002-04", equal to the 16. field of the GDC MAF file) </li>
                                    <li>matched_norm_sample_barcode (i.e., the BCR aliquot barcode for the matched normal sample, e.g., "TCGA-02-0021-10A-01D-0002-04", equal to the 17. field of the GDC MAF file)</li>
                                    <li>match_norm_seq_allele1 (i.e., the matched normal sequencing allele 1, e.g., "T", equal to the 18. field of the GDC MAF file)</li>
                                    <li>match_norm_seq_allele2 (i.e., the matched normal sequencing allele 2, e.g., "ACGT", equal to the 19. field of the GDC MAF file)</li>
                                    <li>tumor_sample_uuid (i.e., the BCR aliquot UUID for the tumor sample, e.g., "b2804bb2-70f4-471a-b6db-70c0ef457df3", equal to the 33. field of the GDC MAF file)</li>
                                    <li>matched_norm_sample_uuid (i.e., the BCR aliquot UUID for the matched normal sample, e.g., "567e8487-e29b-32d4-a716-446655443246", equal to the 34. field of the GDC MAF file)</li>
                                    </ol>
 Download date	2018-12-12T08:20:39.542+01:00
Average region length	1.06
Number of regions	2706469
Number of samples	10187
Size	648.59 MB
Upload date	2018/12/19 21:21:30