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kyizhak / RNA_MUTECT_1.0

BSD 3-Clause "New" or "Revised" License
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Using RNA-MuTect with MuTect2 #2

Open ikarus97 opened 5 years ago

ikarus97 commented 5 years ago

Hi, we're trying your pipeline with somatic mutations from MuTect2 (gatk-4.0.8.1).

It doesn't look like to have option '-U ALLOW_N_CIGAR_READS'. We are still in Step 1 (realignment step), but will it be a problem in later steps?