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Phred scale clarifications #579

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Phred scale clarifications #579

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Commits on Nov 11, 2021

  1. Be more explicit on phred scale definition.

    @jkbonfield
    jkbonfield committed Nov 11, 2021
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  2. Clarify the multiple incompatible uses of "phred-scale". 

    Sometimes this refers to $10 log_{10}(p)$, sometimes to $10
log_{10}(1-p)$, and sometimes to something normalised so $p$ isn't
really a probability at all.

Note CNL, CNP and CNQ don't mention phred anywhere in their
short description and only Phred in the long description for CNQ, so
I applied the same logic to PL, PP (is this correct?) and PQ.

Also clarified the "VCF tag naming conventions" part.  I changed
phred-scale in one part there to phred-true-scale.  I'm not so happy
with that, but as it's immediately followed by the formula I think
it's clear.
    @jkbonfield
    jkbonfield committed Nov 11, 2021
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  3. Replaced $log_{10}$ with $\log_{10}$ for improved formatting in VCF.

    @jkbonfield
    jkbonfield committed Nov 11, 2021
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