Can you please provide
a) GATK 18.104.22.168
in this post, you confirm the value of indel realignment, even haplotypecaller incleding some of that, so why gatk not including it, we want a good command, but not continous new command that not much useful, I still do not know why gatk3 can include indel realignment, but why gatk4 can not. ,command like calling complex variant is also we needed, I think developers may pay some time on this, thanks a lot
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