RNC is ".." on site with DP=1, but it's "D." on site with DP=2

[esctrionsit]

Hi,

I'm using glnexus to do the joint call on gvcfs generated by GATK, and it is part of a SNP calling pipeline for NGS data with a sequencing depth of ~1×. During reading the pVCFs, I found that the genotype on some variations are successfully called, even if the DP on the site is only one (e.g. red boxes in the image), while genotypes on some other sites with DP=2 are called as half call with the RNC="D." (e.g. blue boxes in the image).

Could you please clarify for me that under what exact condition the glnexus would give a half call with the RNC="D."? Thanks!

Sincerely,
Wang