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vt normalize specifications

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Unique identifier OMICS_07615
Name vt normalize
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Hyun Min Kang

Publication for vt normalize

vt normalize citations

 (5)
library_books

A review of somatic single nucleotide variant calling algorithms for next generation sequencing data

2018
Comput Struct Biotechnol J
PMCID: 5852328
PMID: 29552334
DOI: 10.1016/j.csbj.2018.01.003

[…] may be reported in seemingly different representations (), making it complicated to compare variant files generated by different variant callers. variant normalization and comparison tools like vt normalize  and vcfeval in rtg tools  are useful for this task.fig. 2, variant calling algorithms have been evolving and improving in the past years. the underlying models are getting […]

library_books

ClinVar data parsing

2017
Wellcome Open Res
PMCID: 5473414
PMID: 28630944
DOI: 10.21956/wellcomeopenres.12572.r22988

[…] latest xml and txt files from clinvar ftp., parse the xml file to extract fields of interest into a flat file., normalize the representation of genome coordinates using our python implementation of vt normalize ., group the allele-trait records by allele to aggregate record information except clinical significance from multiple submitters, independent of conditions. join the txt file […]

library_books

Evaluating Variant Calling Tools for Non Matched Next Generation Sequencing Data

2017
Sci Rep
PMCID: 5324109
PMID: 28233799
DOI: 10.1038/srep43169

[…] all the other tools report distinct mutations., a comprehensive combined evaluation of the different variant calling tools’ output would therefore require normalization (e.g. with the help of “vt normalize”) of the output of every variant calling tool., all variant calling tools can be easily downloaded and installed. analysis of the 54 illumina hiseq samples (first dataset) and the 111 […]

library_books

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

2016
Genome Biol
PMCID: 4901422
PMID: 27286965
DOI: 10.1186/s13059-016-0985-1

[…] []. haplotypes and other complex variants were decomposed using vcflib vcfallelicprimitives v1.0.0-rc0 (https://github.com/ekg/vcflib/releases/tag/v1.0.0-rc0) followed by normalisation using vt normalize v0.57 []. the resulting vcf file was filtered with the following parameters: dp > 10 & mqm > 30 & qual > 1 & qual/ao > 10 & saf > 2 & sar > 2 & […]

library_books

A somatic reference standard for cancer genome sequencing

2016
Sci Rep
PMCID: 4837349
PMID: 27094764
DOI: 10.1038/srep24607

[…] values above 2 represent a gain and values below are losses., the truth set for each growth was constructed by compiling variants called from each pipeline. small variants were normalized using vt-normalize to address the issues of left alignment and parsimony. we define an snv variant biomarker as “chromosome:start location:reference:alternate”. single nucleotide polymorphisms (snps) […]


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vt normalize institution(s)
Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA

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