Count of reads with mapping quality zero for each sample
FORMAT=<ID=MQ0,Number=1,Type=Integer,Description="Number of Mapping Quality Zero Reads per sample">
This annotation gives you the count of all reads that have MAPQ = 0 for each sample. 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 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.