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Why VCF use RMS quality?

stephenstephen Member
edited August 2012 in Ask the GATK team

Hi,

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?

Thank you.

Best Answer

  • ebanksebanks Broad Institute ✭✭✭✭
    Accepted Answer

    Hi Stephen,

    The RMS is the standard defined and used in the VCF specification. I suppose if you have an issue with it, then you should contact the list for the VCF spec.

    The GATK could very easily add another INFO field for the mean quality. You would just need to implement an Annotation to do this - which would be very simple given that it's almost exactly like the RMSMappingQuality Annotation (so it's mostly a matter of copying and pasting). Good luck!

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    Hi Stephen,

    The RMS is the standard defined and used in the VCF specification. I suppose if you have an issue with it, then you should contact the list for the VCF spec.

    The GATK could very easily add another INFO field for the mean quality. You would just need to implement an Annotation to do this - which would be very simple given that it's almost exactly like the RMSMappingQuality Annotation (so it's mostly a matter of copying and pasting). Good luck!

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