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