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Vt (view source)

Revision as of 16:17, 4 December 2013

110 bytes added ,  16:17, 4 December 2013
→‎View
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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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Views a VCF or BCF or VCF.GZ file.  Eventually to support filters, subsetting of samples.
 
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   #merge duplicate variants and save output in mills.merged.vcf
 
   #merge duplicate variants and save output in mills.merged.vcf
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   vt mergedups mills.vcf -o mills.merged.vcf
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   vt view mills.vcf  
 
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  usage : vt mergedups [options] <in.vcf>
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usage : vt view [options] <in.vcf>
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  options : -o  output VCF file [-]
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options : -o  output VCF file [-]
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            -p  merge by position [false]
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          -v  variant type []
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          -p  print options and summary []
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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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