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Test-drive the GATK tools and Best Practices pipelines on Terra
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Threshold for base phred quality
Hi, when I looked at the call_stats output from MuTect, I am wondering does MuTect only count the reads with base phred quality > 5 in the t_ref_count, t_alt_count, n_ref_count, n_alt_count fields? (I got this conclusion by looking at the base phred quality of each read in IGV). If so, is there any way to change the threshold for the base phred quality? Thanks!