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=== Normalization ===
=== Normalization ===
[http://genome.sph.umich.edu/wiki/Variant_Normalization Normalize] variants in a VCF file.
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[http://genome.sph.umich.edu/wiki/Variant_Normalization Normalize] variants in a VCF file.
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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.
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vt normalize <input.vcf> -r <sequence.fa> -o <output.vcf>
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#
vt normalize mills.vcf -r seq.fa -o -
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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=== Merge duplicate variants ===
=== Merge duplicate variants ===
