HaplotypeScore missing values

Dear "the team",
I understand from the 1KG paper that you used HaplotypeScore to filter variants using multiple variable Gaussian distribution. However, GATK does not output HaplotypeScore for all variants. How can you handle variants without haplotypescores? Did you assume that haplotypescores of the variants are 0 or something?
thank you very much,
best regards,

Si Quang Le

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