deepvariant: NoCall with missing PL value

Hi,

I am using Pepper-MARGIN-DeepVariant r0.7 with custom made models for Pepper-SNP, Pepper-HP and DeepVariant. As far as I know, this release uses DeepVariant 1.2.

I have run this pipeline successfully for a small cohort of about 100 genomes but when merging the GVCF files, GLnexus 1.4.1 (with config DeepVariant) complains that at least one variant is missing PL values. I tracked down the issue to one GVCF were the record is:

CHR	POS	.	A	G,<*>	9.9	NoCall	.	GT:GQ:DP:AD:VAF:PL	./.:0:5:0,0,0:0,0:0,0,990,990,990

We can see that this GVCF record has 5 PL values where there should be 6. The corresponding record in the VCF file is:

CHR POS .	A	G	9.9	refCall	.	GT:GQ:DP:AD:VAF:C	./.:0:5:0:0:DV

The VCF record indicates that the variant call was issued by DeepVariant.

Any ideas what could be the issue here?

Thank you for your help, Guillaume