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annotate vcf file

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 (.)

annovar annotation
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written by arwa.ahmad95 • arwa.ahmad95

1 answer

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

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written by Istvan Albert Istvan Albert

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?

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written by arwa.ahmad95 • arwa.ahmad95

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