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  • how to get quality information from VarScan mpileup2snp

    So, I know you can get map and base quality information as output when running varscan pileup2snp, but why don't you get this output when running mpileup2snp?

    I see it says, for MapQual1 and MapQual2 'only useful if in pileup' but I don't understand. Why can't I get this information from a multi sample pileup?

    Thank you.

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