Count of all reads with MAPQ = 0 across all samples
INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
This anotation gives you the count of all reads that have MAPQ = 0 across all samples. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.
It is not useful to apply this annotation with HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation will always return a value of 0.
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.