Meaning of MQ value

Menno

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

tommycarstensen

Hi Menno,

This might be helpful:
https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_MappingQualityRankSumTest.php

"The value output for this annotation is the u-based z-approximation from the Mann-Whitney-Wilcoxon Rank Sum Test for mapping qualities (MAPQ of reads supporting REF vs. MAPQ of reads supporting ALT)."

Tommy

Geraldine_VdAuwera

To add to Tommy's answer, MQ is tricky because the primary statistic that it's calculated from, MAPQ, is not a well-calibrated measurement.

More generally, for guidance on selecting thresholds appropriate for your data empirically, see this article.

Sheila

@Menno
Hi Menno,

Also, have a look at the documentation.

-Sheila