Hi, Your work is wonderful.I am trying to run this pipeline. But I don't understand this "3. A MAF file listing inital set of mutations called by MuTect with the '-U ALLOW_N_CIGAR_READS' flag", In this part, run MuTect need a input_file:tumor Tumor.cleaned.bam, is this bam file come from "2. RNA BAM file aligned with STAR. Parameters used to run STAR are found in Supplementary Table 12." ? I need your help. Thanks a lot.
Hi, Your work is wonderful.I am trying to run this pipeline. But I don't understand this "3. A MAF file listing inital set of mutations called by MuTect with the '-U ALLOW_N_CIGAR_READS' flag", In this part, run MuTect need a input_file:tumor Tumor.cleaned.bam, is this bam file come from "2. RNA BAM file aligned with STAR. Parameters used to run STAR are found in Supplementary Table 12." ? I need your help. Thanks a lot.