MC3 pipeline 是保守的,试图删除所有假阳性的germline calling 。TCGA LAML AWG创建的原始MAF的大部分都是通过手工干预获得的,包括不包含在TCGA数据目录中的Sanger测序数据,以恢复原本未调用的变量。因此,open-access 的MC3 call set 仅占原始MAF中variant call 的44%。 Effects of Somatic Filtering for Open-Access...
Example: Loading TCGALUADcohort. Note that by default MAF from MC3 study is returned > TCGAmutations::tcga_load(study ="LUAD") Loading LUAD. Please cite: https://doi.org/10.1016/j.cels.2018.03.002forreference An object of class MAF ID summary Mean Median1: NCBI_BuildNANANA2: CenterNANA...