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#normalize variants and write out to mills.normalized.vcf
vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf
vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf
#normalize variants, send to standard out and remove duplicates.
#normalize variants, send to standard out and remove duplicates.
vt normalize mills.vcf -r seq.fa | vt merge_duplicate_variants - -o mills.normalized_merged.vcf
vt normalize mills.vcf -r seq.fa | vt merge_duplicate_variants - -o mills.normalized_merged.vcf
