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Vt

74 bytes added, 16:48, 5 October 2015
Annotate Indels
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
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