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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Meaning of MQ value
Dear GATK team,
I am wondering: is there an easy way to interpret the MQ value?
I know that MQ stands for the 'root mean square (RMS) of Mapping Quality', and that it gives 'an estimation of the overall mapping quality of reads supporting a variant call'.
But is there a kind of relation, similar to a Phred score, between the observed MQ value and the probability that the variant call is erroneous?
I am asking because I wonder which MQ values to consider acceptable. (I am aware that the GATK webpage (http://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set) suggest a MQ-threshold of 40.)
Thanks a lot in advance for your response.
All the best,
Menno de Jong