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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/2015/02/19/bioinformatics.btv112.abstract?keytype=ref&ijkey=2kB1TkBGzkoP1gd (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/2015/02/19/bioinformatics.btv112.abstract?keytype=ref&ijkey=2kB1TkBGzkoP1gd (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
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.
of 1000 base pairs.
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options : -o output VCF file [-]
options : -o output VCF file [-]
-I file containing list of intervals []
-I file containing list of intervals []
-w window size for local sorting of variants [1000]
-i intervals []
-i intervals []
-r reference sequence fasta file []
-r reference sequence fasta file []
