Missing MQ scores in gvcf
I am trying to hard filter my vcf and I am using:
module load gatk/4.0.6
gatk VariantsToTable -V diploid_genotyped_v102220.g.vcf -F MQ -O diploid_genotyped_unfiltMQ_v102220.txt
The resulting file contains all NA's.
What is happening here!?!
Heather Tuttle could you post the stack trace of your VariantsToTable command so we can check if there were any issues?
Also, were there NAs in any specific column? Did any of the data get transferred?
I have tried recalling haplotypes with -A RMSMappingQuality and going through the pipeline again, and still no MQ. MQ is a standard annotation usually, right? I am able to get every other annotation just fine with VtoT, even MQ rank sum! Below is the stack trace
MQ is also not in the VCF, whereas everything else is. I noticed that I was using haplotypecaller 4.1.2 and then using combineGVCF and GenotypeGVCF 4.0.6. Could this be the issue?
Hi Heather Tuttle, please see this resource for troubleshooting about why it may not exist: Missing annotations in the output callset VCF
I would also recommend using a newer version of GATK than 4.0.6 because there have been many improvements since then, but I am not sure it will solve this issue.
That really doesn't help me at all. It does not tell me why MQ scores are missing or why they are not being transferred to the VCF from the bam. The scores are all present in the bams! I have run 4.0.6 and 4.1.2 and have had no luck. I have run with and without -A RMSMappingQuality and no luck. Nothing on any stack trace. MQ is really important. what do you suggest I do?
Hi Heather Tuttle, thanks for checking that troubleshooting document. I think I may have found what is causing the issue. The RMSMappingQuality annotation had an issue when being calculated from GVCFs created with older GATK versions.
You could either re-create your GVCF with the newest version of GATK, or use the option --allow-old-rms-mapping-quality-annotation-data when adding the annotation.
More info can be found in the GATK 188.8.131.52 release notes.
Hope this helps!
I will request to update to the newest version of GATK from the supercomputing institute that I work with. Until then, I will try using the flag and give an update! Thanks!
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