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