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Revision as of 11:38, 20 November 2013

375 bytes added ,  11:38, 20 November 2013
→‎Merge duplicate variants
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=== Merge duplicate variants ===
 
=== Merge duplicate variants ===
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Merges duplicate variants by position with the option of considering alleles.  (This just discards the duplicate variant that appears later in the VCF file)
 
Merges duplicate variants by position with the option of considering alleles.  (This just discards the duplicate variant that appears later in the VCF file)
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<div class="mw-collapsible-content">
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Normalized variants may have their positions changed; in such cases, the normalized variants
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are reordered and output in an ordered fashion.  The local reordering takes place over a window
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of 10000 base pairs.
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</div>
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</div>
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<div class=" mw-collapsible mw-collapsed">
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  vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf
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   Options:
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   #merge duplicate variants and save output in mills.merged.vcf
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    : Input VCF file
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   vt mergedups mills.vcf -o mills.merged.vcf
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   -o,  --output-vcf <string> : Output VCF file [-]
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   -p,  --merge-by-position  : Merge by position [false]
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   usage : vt mergedups [options] <in.vcf>
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   Example:
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   options : -o  output VCF file [-]
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  e.g. vt merge_duplicate_variants -i 8904indels.dups.genotypes.vcf -o out.vcf
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            -p merge by position [false]
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  e.g. vt merge_duplicate_variants -p -i 8904indels.dups.genotypes.vcf -o out.vcf
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= Maintained by =
 
= Maintained by =
    
This page is maintained by  [mailto:atks@umich.edu Adrian]
 
This page is maintained by  [mailto:atks@umich.edu Adrian]
Atks
1,102

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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/8986"

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