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#normalize variants, send to standard out and remove duplicates.
#normalize variants, send to standard out and remove duplicates.
vt normalize dbsnp.vcf -r seq.fa | vt uniq - -o dbsnp.normalized.uniq.vcf
vt normalize dbsnp.vcf -r seq.fa | vt uniq - -o dbsnp.normalized.uniq.vcf
#read in variants that do not contain N in the explicit alleles, normalize variants, send to standard out.
vt normalize dbsnp.vcf -r seq.fa -f "~VARIANT_CONTAINS_N"
#variants that are normalized will be annotated with an OLD_VARIANT info tag.
#variants that are normalized will be annotated with an OLD_VARIANT info tag.
