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Vt

2,661 bytes added, 15:47, 5 October 2015
Merge candidate variants
-- ignores the rest of the labeled arguments following this flag
-h displays help
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=== Annotate Indels ===
 
Annotates indels with VNTR information and adds a VNTR record.
 
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#annotates indels from VCFs with VNTR information.
vt annotate_indels in.vcf -r hs37d5.fa -o annotated.sites.vcf
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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
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