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Old 07-10-2012, 06:18 PM   #1
alg
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Location: England

Join Date: Jul 2012
Posts: 2
Default 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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