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Does VariantAnnotator --dbsnp take care of strand flips and/or discrepancies in the REF alleles?
I'm using GATK VariantAnnotator --dbsnp to populate the ID column of a WGS VCF with SNP IDs from a GWAS summary stats file. I was wondering if GATK VariantAnnotator --dbsnp does take care of possible strand flips, and other discrepancies regarding which allele is the REF (and which one is the ALT allele), etc., or if it actually requires REF and ALT alleles to be exactly the same between the --dbsnp file and the input VCF for the annotation.