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