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which is the best way to see ALL the nucleotides in EVERY position of a target?
I would like to ask you which is the best way to see ALL the nucleotides in EVERY position of a target. I used EMIT_ALL_SITES option with UnifiedGenotyper but the output miss an information: I obtain the genotype and the coverage but no information about other possible nucleotides present but not called (for example 148 G and 2 T with genotype 0/0 and DP 150). Can you help me?
Thank you in advance