Mixing up GATK versions

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wannamd

• November 25, 2020 02:43
• Edited

a) GATK version used: 4.1.7.0

b) Exact command used:

gatk --java-options "-Xmx8g" GenotypeGVCFs\

-R hg38.fa \

-V input.g.vcf \

-O output.vcf

c) Entire error log:

A USER ERROR has occurred: Bad input: Presence of '-RAW_MQ' annotation is detected. This GATK version expects key RAW_MQandDP with a tuple of sum of squared MQ values and total reads over variant genotypes as the value. This could indicate that the provided input was produced with an older version of GATK. Use the argument '--allow-old-rms-mapping-quality-annotation-data' to override and attempt the deprecated MQ calculation. There may be differences in how newer GATK versions calculate DP and MQ that may result in worse MQ results. Use at your own risk.

Ok, so I am aware that I am not supposed to be mixing GATK versions whilst going through single analysis pipeline. However, I received a sample in GVCF file called with GATK version 4.0.5.1 and for the required analysis, I need to convert the GVCF file to a VCF file with GATK version 4.1.7, as that is what I have on my server. 

I tried running the above command line and I get a warning message, which I am assume is from mixing up different GATK versions on the same file. However, it still gives me the option of ignoring the message and going through with the command and I was wondering if this version difference will make a significant difference? (for this particular job - converting g.vcf to vcf) Any help would be greatly appreciated. Thanks!

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• Official comment

  

  Genevieve Brandt (she/her)

  • July 28, 2021 01:24

  Hi wannamd,

  In order to run this step successfully without recreating your GVCFs you will need to use the --allow-old-rms-mapping-quality-annotation-data argument. You can still proceed just fine but the warning is letting you know that your MQ annotation results may not be reliable so you should use other annotations to reference the quality of your variant calls.

  Best,

  Genevieve

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  Anton Kovalsky

  • November 25, 2020 23:51

  Hi wannamd

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

   

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