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Why VCF use RMS quality?
I have a question about VCF format.
In the INFO field, both the sub-fields MQ and BQ use RMS (root mean square) to summarize the quality scores.
RMS is useful to deal with the data having both positive and negative values,
but it will inflate the extreme values (ex: the RMS for (50,50) is 50, but it is about 70 for (1,99))
that may make some skew on the intuitive understanding to the result.
I see both GATK 1.4 and 2.0 generates MQ and BQ fields.
Since the Phred score should always be positive, could GATK add another field simply for the mean of quality?