I am using BWA MEM 0.7.17 for all my paired-end alignments.
Can someone clue me in on why some alignments have a
MQ tag and others do not?
The commands are identical in some cases. Does BQSR apply this tag, there could be a difference in the options at this step perhaps? And I think some alignments use GATK 3.7 or earlier and others with the MQ tag has GATK 3.8