Difference between revisions of "Vt"
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=== Normalization === | === Normalization === | ||
− | [http://genome.sph.umich.edu/wiki/Variant_Normalization Normalize] variants in a VCF file. | + | <div class=" mw-collapsible mw-collapsed" style="width:800px"> |
+ | [http://genome.sph.umich.edu/wiki/Variant_Normalization Normalize] variants in a VCF file. | ||
+ | <div class="mw-collapsible-content"> | ||
+ | Normalized variants may have their positions changed; in such cases, the normalized variants | ||
+ | are reordered and output in an ordered fashion. The local reordering takes place over a window | ||
+ | of 10000 base pairs. | ||
+ | </div> | ||
+ | </div> | ||
− | + | <div class=" mw-collapsible mw-collapsed" style="width:800px"> | |
+ | vt normalize <input.vcf> -r <sequence.fa> -o <output.vcf> | ||
+ | <div class="mw-collapsible-content"> | ||
+ | # | ||
+ | vt normalize mills.vcf -r seq.fa -o - | ||
+ | vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf | ||
+ | vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf | ||
+ | </div> | ||
+ | </div> | ||
=== Merge duplicate variants === | === Merge duplicate variants === |
Revision as of 17:17, 21 October 2013
Introduction
vt is a variant tool set that discovers short variants from Next Generation Sequencing data. The features are being rolled out to github as major rewriting is being undertaken.
Location
The source files are housed in github.
git clone https://github.com/atks/vt.git
Common options
-i multiple intervals in <seq>:<start>-<end> format delimited by commas.
-I multiple intervals in <seq>:<start>-<end> format listed in a text file line by line.
-o defines the out file which and has the STDOUT set as the default. You may modify the STDOUT to output the binary version of the format.
Programs
Normalization
Normalize variants in a VCF file.
Normalized variants may have their positions changed; in such cases, the normalized variants are reordered and output in an ordered fashion. The local reordering takes place over a window of 10000 base pairs.
vt normalize <input.vcf> -r <sequence.fa> -o <output.vcf>
# vt normalize mills.vcf -r seq.fa -o - vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf vt normalize mills.vcf -r seq.fa -o mills.normalized.vcf
Merge duplicate variants
Merges duplicate variants by position with the option of considering alleles. (This just discards the duplicate variant that appears later in the VCF file)
Options: -i, --input-vcf <string> : Input VCF file -o, --output-vcf <string> : Output VCF file [-] -p, --merge-by-position : Merge by position [false]
Example: e.g. vt merge_duplicate_variants -i 8904indels.dups.genotypes.vcf -o out.vcf e.g. vt merge_duplicate_variants -p -i 8904indels.dups.genotypes.vcf -o out.vcf
Maintained by
This page is maintained by Adrian