Changes

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   #annotates the variants found in mills.vcf

   #annotates the variants that overlap with coding regions.

   vt annotate_regions mills.vcf -b coding.bed.gz -t CDS -d "Coding region"

   vt annotate_regions mills.vcf -b coding.bed.gz -t CDS -d "Coding region"

  #annotates variants with the following fields

  #annotates the variants that overlap with low complexity regions.

  ##INFO=<ID=CDS,Number=0,Type=String,Description="Coding Region">

  vt annotate_regions mills.vcf -b mdust.bed.gz -t DUST -d "DUST Low Complexity Region"

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