No base called when reference is ambiguous

[snacktavish]

We are finding that when there is an ambiguity code in the reference (e.g an N), even if a base is called in the the mpileup step, that base is not reported in bcftools call -c output.

bcftools mpileup -f best_ref.fas best_sorted.bam -o best_sorted.vcf

in the best_sorted.vcf we have a base call at position 1855, e.g. NODE_56 1855 . N C,<*> 0 . DP=30;I16=0,0,16,12,0,0,1003,36369,0,0,1232,54208,0,0,570,13518;QS=0,1,0;VDB=0.338343;SGB=-0.693054;MQSB=1;MQ0F=0 PL 255,84,0,255,84,255

bcftools call -c best_sorted.vcf -o best_cns.vcf

That base call does not show up in the consensus.vcf

NODE_56  	1856	.	A	.	113.995	.	DP=30;MQSB=1;MQ0F=0;AF1=0;AC1=0;DP4=15,13,0,0;MQ=44;FQ=-110.987	GT:PL	0/0:0
NODE_56         1857	.	A	.	113.995	.	DP=31;MQSB=1;MQ0F=0;AF1=0;AC1=0;DP4=14,14,0,0;MQ=44;FQ=-110.987	GT:PL	0/0:0```


Are we missing a flag or something?

Thank you, (cc @jtoscanifield )