after gatk VariantAnnotator -V *_com_norm.vcf -A AlleleFraction -O *_norm_AB.vcf There "nan,nan" or "nan" in my vcf file

Question

[zhuo]

After I run this code

gatk VariantAnnotator -V *_com_norm.vcf -A AlleleFraction -O *_norm_AB.vcf

There are nan,nan or nan in my vcf file

The input file doesn't have nan,nan or nan, it (*_com_norm.vcf) comes form merging (bcftools merge) 3 different vcf files.

Can someone help me?

Thanks very much

gatk VariantAnnotator -V *_com_norm.vcf -A AlleleFraction -O *_norm_AB.vcf