The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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