TCGA数据库maf突变资料官方大全

因为TCGA计划跨时太长，这些年找somatic变异的软件也很多，所以TCGA团队下功夫在计划结束后（April 2018）完整的系统性的整理了最后的somatic突变数据。依托于文章：[Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines]() March 201810.1016/j.cels.2018.03.002

The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different cancer types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling in Multiple Cancers project, our effort to generate a comprehensive encyclopedia of somatic mutation calls for the TCGA data to enable robust cross-tumor-type analyses. Our approach accounts for variance and batch effects introduced by the rapid advancement of DNA extraction, hybridization-capture, sequencing, and analysis methods over time. We present best practices for applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. The dataset created by this analysis includes 3.5 million somatic variants and forms the basis for PanCan Atlas papers.The results have been made available to the research community along with the methods used to generate them. This project is the result of collaboration from a number of institutes and demonstrates how team science drives extremely large genomics projects.纳入的软件Deposited DataMC3 Fileshttps://gdc.cancer.gov/about-data/publications/mc3-2017Software and AlgorithmsMuTecthttps://github.com/broadinstitute/mutectPindelhttps://github.com/genome/pindelRadiahttps://github.com/aradenbaugh/radiaVarScan2http://dkoboldt.github.io/varscan/SomaticSniperhttps://github.com/genome/somatic-sniperMuSEhttps://github.com/danielfan/MuSEIndelocatorhttp://archive.broadinstitute.org/cancer/cga/indelocatorMaf2Vcfhttps://github.com/covingto/vcf2maf/

文章资料下载GDC ManifestsOpen-Access Data - Download Manifest (6 Files)MAF FilesMC3 Public MAF - mc3.v0.2.8.PUBLIC.maf.gzReference FilesReference Data - ref_data_for_oxog_all_permissions.tar.gzReference Data - 2 - ref_data_for_oxog.tarTarget Region BED File - gencode.v19.basic.exome.bedgaf_20111020Plusbroad_wex_1.1_hg19.bed - gaf_20111020Plusbroad_wex_1.1_hg19.bed其它类似研究TCGA计划是最出名的肿瘤研究计划，其它也有一些优秀者值得关注ProjectMethodSample Count (Approx.)TCGA MC3exome10,000GENIE44 gene panel19,000ICGC PCAWGwhole genome2,800100,000 Genomes Projectwhole genomeprojected: 100,000CCLEexome950Targetexome700Foundation medicine306 gene panel18,000写在最后