Annotate ALT field with N as a value

[Titorat]

I am working on annotating a vcf file using a bcf dbSNP. But it seems that records with N as an ALT field don't get annotated. But surprisingly to me, records with false A,G,C, or T characters get annotated and corrected. I assume there is a place where this logic is implemented, but I can't find it. Can you point me to why this happens? Also I inspected the vcf_setter_al code here https://github.com/samtools/bcftools/blob/develop/vcfannotate.c with no luck.

Thanks in advance

[pd3]

I don't understand the question completely. I can see how it'd be possible that N's in ALT column will not be matched well, but don't understand the part with "false" A,C,G,T.

Any chance you could create a small test case that would highlight the observed and expected behavior?