I started using GATK v22.214.171.124 on some of my WGS samples some days back. Few samples got a bug- "HaplotypeCaller exception: contig must be non-null and not equal to *, and start must be >= 1". I checked online and found that this bug was solved in the new sub-version. I downloaded GATK v126.96.36.199 and started running it on the unsuccessful samples.
Mostly, new versions (not sub-versions) get released when there is a major change in the code/algorithm of the tool. This is a common thing in bioinformatics community that new versions of tools get released, bugs get reported and then new sub-versions get released within a span of few days/months leaving the users in a fix.
In my case, the inherent algorithm did not change, only some bugs got solved. Should I be running the updated sub-version of the tool on the successful samples again so that a commonality is maintained? Although, the final output will not change. Or, should I just write while reporting the procedure that GATK 4.0 was used, and not mention the sub-version at all. What is the best practice that should be followed in this case?