Changes

   vt normalize <input.vcf> -r <sequence.fa> -o <output.vcf>

   vt normalize <input.vcf> -r <sequence.fa> -o <output.vcf>

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   #

   #normalize variants, send to standard out and remove duplicates.

  vt normalize mills.vcf -r seq.fa -o -

   vt normalize mills.vcf -r seq.fa -o - | vt merge_duplicate_variants - -o mills.normalized_merged.vcf

   vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf

  vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf

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