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Vt (view source)

Revision as of 16:47, 5 October 2015

2,661 bytes added ,  16:47, 5 October 2015
→‎Merge candidate variants
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             --  ignores the rest of the labeled arguments following this flag
 
             --  ignores the rest of the labeled arguments following this flag
 
             -h  displays help
 
             -h  displays help
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</div>
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</div>
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=== Annotate Indels ===
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Annotates indels with VNTR information and adds a VNTR record.
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<div class=" mw-collapsible mw-collapsed">
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  #annotates indels from VCFs with VNTR information.
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  vt annotate_indels in.vcf -r hs37d5.fa -o annotated.sites.vcf
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<div class="mw-collapsible-content">
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  usage : vt annotate_indels [options] <in.vcf>
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  options : -v  add vntr record [false]
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          -x  override tags [false]
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          -f  filter expression []
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          -d  debug [false]
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          -m  mode [f]
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              e : by exact alignment              f : by fuzzy alignment
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          -c  classification schemas of tandem repeat [6]
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              1 : lai2003   
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              2 : kelkar2008 
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              3 : fondon2012 
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              4 : ananda2013 
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              5 : willems2014
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              6 : tan_kang2015
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          -a  annotation type [v]
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              v : a. output VNTR variant (defined by classification).
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                    RU                    repeat unit on reference sequence (CA)
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                    MOTIF                canonical representation (AC)
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                    RL                    repeat tract length in bases (11)
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                    FLANKS                flanking positions of repeat tract determined by exact alignment
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                    RU_COUNTS            number of exact repeat units and total number of repeat units in
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                                          repeat tract determined by exact alignment
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                    FZ_RL                fuzzy repeat tract length in bases (11)
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                    FZ_FLANKS            flanking positions of repeat tract determined by fuzzy alignment
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                    FZ_RU_COUNTS          number of exact repeat units and total number of repeat units in
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                                          repeat tract determined by fuzzy alignment
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                    FLANKSEQ              flanking sequence of indel
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                    LARGE_REPEAT_REGION  repeat region exceeding 2000bp
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                  b. mark indels with overlapping VNTR.
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                    FLANKS      flanking positions of repeat tract determined by exact alignment
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                    FZ_FLANKS    flanking positions of repeat tract determined by fuzzy alignment
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                    GMOTIF      generating motif used in fuzzy alignment
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                    TR    position and alleles of VNTR (20:23413:CACACACACAC:<VNTR>)
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              a : annotate each indel with RU, RL, MOTIF, REF.
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          -r  reference sequence fasta file []
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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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          -?  displays help
 
  </div>
 
  </div>
 
</div>
 
</div>
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