Missing MQ tag from bwa mem alignments

Question

[QVINTVS_FABIVS_MAXIMVS]

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

Thank you.

Answer 1

[benformatics]

Older versions of GATK (i.e. pre-4.x), and thus the bugs they contain, are no longer officially supported.

The missing MQ likely involves an incompatibility when combining VCFs. There doesn’t seem to be a retroactive solution.

https://gatkforums.broadinstitute.org/gatk/discussion/4618/mq-annotation-missing

[QVINTVS_FABIVS_MAXIMVS]

I was referring to SAM/BAM file MQ tag. Unfortunately sometimes I have to use legacy code.