annotate vcf file

Question

[arwa.ahmad95]

I annotate my vcf file using ANNOVAR but when I open the annotate vcf , I found some annotating columns ( such as Gene. refGene .... ) consist of (.) what is mean (.)

Answer 1

[Istvan Albert]

Dots usually mean empty value, dots are inserted to mark the empty column,

otherwise when tools split on whitespace carelessly the columns can end up out of order

[arwa.ahmad95]

but if (.) in allel frequency for specific database why it appears? I don't understand why it's appear in another way, why not calculate the allel frequency?