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about combine GVCFs

after filtering the vcf files with ISHet Filter, I am using the command CombineGVCFs as follows:
.././gatk CombineGVCFs -R reference.fasta --variant filtered1.g.vcf --variant filtered2.g.vcf --variant filtered3.snps.g.vcf -O combined.vcf

The input vcf files have thousands of SNPs but after combining these files, there is no SNP in the OUTPUT file. why is so? Kindly guide me .

I am using vGATK4.1.0.0


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