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