Changes

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[http://genome.sph.umich.edu/wiki/Variant_Normalization Normalize] variants in a [http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42 VCF]  file [http://bioinformatics.oxfordjournals.org/content/early/2015/03/22/bioinformatics.btv112 (Tan et al. 2015)] .  Normalized variants may have their positions changed; in such cases, the normalized variants

[http://genome.sph.umich.edu/wiki/Variant_Normalization Normalize] variants in a [http://www.1000genomes.org/wiki/analysis/variant-call-format/vcf-variant-call-format-version-42 VCF]  file [http://bioinformatics.oxfordjournals.org/content/early/2015/03/22/bioinformatics.btv112 (Tan et al. 2015)] .  Normalized variants may have their positions changed; in such cases, the normalized variants

are reordered and output in an ordered fashion.  The local reordering takes place over a window of 10000 base pairs which may be changed via the -w option.

are reordered and output in an ordered fashion.  The local reordering takes place over a window of 10000 base pairs which may be changed via the -w option.  There is an underlying assumption that the REF

field is consistent with the reference sequence use, vt will check for this and will fail if reference inconsistency is encountered; this may be relaexd with the -n option.

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             -d  debug [false]

             -d  debug [false]

             -q  do not print options and summary [false]

             -q  do not print options and summary [false]

             -w  window size for local sorting of variants [10000]

             -w  window size for local sorting of variants [10000]

             -I  file containing list of intervals []

             -I  file containing list of intervals []