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short read preprocessing in MuTect
Hi, I am using MuTect on paired tumor/normal exome data. MuTect pre_process low quality reads before somatic SNV discovery. How can I get the processed bam files? I know there is source code for MuTect at github, but I am not sure which java files are used in preprocessing steps. Can you please tell me the program files for low-quality reads preprocessing? Thanks very much for your time!