I did Genotype refinement process as belows.
$GATK4_CMD --java-options "-Xms8g -Xmx8g" \
-supporting 1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf \
-V filtered.vcf.gz \
Then, there are so weird results.
1. This is HaplotypeCaller result.
2. This is Variant recalibrated result.
3. After genotype refinement, the genotype was changed.
from non-call genotype (./.) to HomVAR variant.
I think this result is so abnormal.