GATK3.8 GenotypeGVCFs MQ abnormal
Hi
We use GATK3.8 GenotypeGVCFs to get 3k population vcf.
we checked the frequency of MQ and found that some sites with MQ higher than 60. Is it abnormal?
MQ frequency by GATK3.8/3.7
The MQ peak from older version 3.3 or GATK4 was perfectly near 60 and few were higher than 60.
MQ frequency by GATK 3.3
Is it the difference between versions?
Comments
1 comment
Hi Qiuju Xia,
Thanks for writing in. You can take a closer look at the changes between GATK versions by viewing the GATK Github release notes page: https://github.com/broadinstitute/gatk/releases
If you search for GenotypeGVCF you should be able to more easily find the changes between different versions. If you still require assistance in understanding the differences, I recommend reaching out to the GATK support team on the GATK forum: https://gatk.broadinstitute.org/hc/en-us/community/topics
If you have any other questions, especially as they relate to the Terra platform, please let us know and we'll be happy to help!
Kind regards,
Jason
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