HaplotypeCaller phased missing genotype to .|.

[Sherry520]

Bug Report

Affected tool(s) or class(es)

gatk HaplotypeCaller --do-not-run-physical-phasing false

Affected version(s)

gatk-4.4.0.0

Description

I used gatk HaplotypeCaller with parameter --do-not-run-physical-phasing false, some missing genotypes were phased to ".|.". What I was expecting was this "./. ", and it will turn to haploid "." after vcftools(0.1.17) recode processing. So, I have to use gatk HaplotypeCaller --do-not-run-physical-phasing true to avoid phasing processing.