if you annotate a vcf with snpeff, how do you know if the annotation are referring to the alternate or reference allele?

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for example I run snpEff my_vcf.vcf

where my_vcf.vcf is

#CHROM    POS    REF    ALT
chr1    97828139    G    A

will give annotation stop_gained. How do I know this is referring to the presence of the alternate allele A. Does `snpEff' really go through and look at ref and alt alleles of does it just update annotation based on position?


annotation


snpsift


snpeff


vep

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