title: Improved VCF normalization for accurate VCF comparison.
abstract: BACKGROUND
  The Variant Call Format (VCF) is widely used to store data about genetic variation. Variant calling workflows detect potential variants in large numbers of short sequence reads generated by DNA sequencing and report them in VCF format. To evaluate the accuracy of variant callers, it is critical to correctly compare their output against a reference VCF file containing a gold standard set of variants. However, comparing VCF files is a complicated task as an individual genomic variant can be represented in several different ways and is therefore not necessarily reported in a unique way by different software.
  
  
  RESULTS
  We introduce a VCF normalization method called Best Alignment Normalisation (BAN) that results in more accurate VCF file comparison. BAN applies all the variations in a VCF file to the reference genome to create a sample genome, and then recalls the variants by aligning this sample genome back with the reference genome. Since the purpose of BAN is to get an accurate result at the time of VCF comparison, we define a better normalization method as the one resulting in less disagreement between the outputs of different VCF comparators.
  
  
  METHODS
  The BAN Linux bash script along with required software are publicly available on https://sites.google.com/site/banadf16.
  
  
  BACKGROUND
  A.Bayat@unsw.edu.au.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.forename: Arash
authors.initials: A
authors.lastname: Bayat
authors.forename: Bruno
authors.initials: B
authors.lastname: Gaëta
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Ignjatovic
authors.forename: Sri
authors.initials: S
authors.lastname: Parameswaran
mesh_terms: D000465:Algorithms; D000483:Alleles; D001483:Base Sequence; D014644:Genetic Variation; D023281:Genomics / Q000379:methods; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software