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Joint-calling with GATK4.1 on gvcf's made with GATK22.214.171.124+
Some version of this question comes up often, with different parts of the GATK workflow with different versions needing to be combined.
In our simple case: we have run Haplotype calling of a study with v 126.96.36.199. We'd like to joint call with v188.8.131.52. In the more complex case: we have two studies, one run with v184.108.40.206 and the next with a slightly later point-release (v4.0.x.y), and we would like to joint-call the two together, preferably with v220.127.116.11.
The general theme of the responses to this kind of question is always cautious, but changes depending on the versions in play and the parts of the pipe in play. The closest answer I've got is this one: https://gatkforums.broadinstitute.org/gatk/discussion/7728/when-there-is-a-gatk-update-when-do-you-know-if-you-should-rerun-old-data.
Can you provide me with a more tailored response?