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The difference of algorithms in HaplotypeCaller between gatk3.8 and gatk 4.0.8.1

Dear GATK team,
I want to known the difference of algorithms in Haplotypecaller between gatk3.8 and gatk 4.0.8.1, is it a big difference? Because some site we called with gatk3.8 HaplotypeCaller , it is a SNP. But called with gatk4.0.8.1 HaplotypeCaller, the SNP site is a big indel region.

Answers

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