Mixing up GATK versionsAnswered
a) GATK version used: 126.96.36.199
b) Exact command used:
gatk --java-options "-Xmx8g" GenotypeGVCFs\
-R hg38.fa \
-V input.g.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 188.8.131.52 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!
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.
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