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Vt (view source)

Revision as of 09:51, 5 December 2013

227 bytes added ,  09:51, 5 December 2013
→‎Merge candidate 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)
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Merge candidate variants across samples.  Each VCF file is required to have the FORMAT flags E and N and should have exactly one sample.
    
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   #merge duplicate variants and save output in mills.merged.vcf
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   #merge candidate variants from VCFs in candidate.txt and output in candidate.sites.vcf
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   vt mergedups mills.vcf -o mills.merged.vcf
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   vt candidate_variants candidates.txt -o candidate.sites.vcf
 
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  usage : vt mergedups [options] <in.vcf>
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  usage : vt merge_candidate_variants [options]  
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  options : -o  output VCF file [-]
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  options : -L  file containing list of input VCF files
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            -p merge by position [false]
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            -o  output VCF file [-]
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            -I file containing list of intervals []
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            -i  intervals
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            --  ignores the rest of the labeled arguments following this flag
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            -h  displays help
 
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/9121"

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