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skipping MarkDuplicates in deep sequencing data
Hi GATK team,
Recently I have been working with deep sequencing data(target capture data,about 200x depth,BAM file was sorted ,about 3.39G size),but I was stucked in Picard MarkDuplicates , it took 85h so far and I expect it will takes more time. So can I skip MarkDuplicates and I want to know if skipping MarkDuplicates would result in some big effects in somatic mutation calling with MuTect?