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Recommendations on using different versions of GATK for variant calling and joint genotyping
Dear GATK Team,
From what I understand, best practices recommend using the same version of GATK for variant calling (with HaplotypeCaller) and joint genotyping (with GenotypeGVCFs). Let's say, we found that GATK v3.4 has a better way of calling/reporting mutli-allelic variant calls. Will it be OK to have used HaplotypeCaller from v3.3 to call variants and then use GenotypeGVCFs from v3.4 to perform joint genotyping?