I created sample gvcfs using GATK v.3 and want to joint genotype those files.
I used GATK v.4 to create a Genomics DB using GenomicsDBimport and it worked well.
But when using GenotypeGVCFs to genotype the database, I got the error:
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
I thus tried to use GenotypeGVCFs with the argument '--allow-old-rms-mapping-quality-annotation-data' and it worked.
Nonetheless, I am wondring about the impact of using this argument and I could not find any information about it.
Is using this argument making GATK v.4 using the same way to calculate MQ as GATK v.3?
Does this argument amount to using GATK v.3 for all other calculations of statistics or solely for the calculation of MQ?
For the downstream filtering, should I use GATK v.3 or v.4?
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