vt normalize specifications

Information


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

Versioning


No version available

Documentation


Maintainer


  • person_outline Hyun Min Kang

Publication for vt normalize

vt normalize citations

 (2)
library_books

EAGLE: Explicit Alternative Genome Likelihood Evaluator

2018
BMC Med Genomics
PMCID: 5918433
PMID: 29697369
DOI: 10.1186/s12920-018-0342-1

[…] sulting BAM format alignment data to call variants with: GATK HaplotypeCaller (3.3.0) [, ], SAMtools mpileup (1.3) [], FreeBayes (1.0.2) [], and Platypus (0.8.1) []. Each callset was normalized using vt normalize [] and the vcfallelicprimitives module in vcflib (https://github.com/ekg/vcflib) to deconstruct complex variants.From the known NS12911 variants, we determined the number of true positive […]

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

[…] g3e35e72 []. 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 & RPR > 1 & RPL > 1 using vcffilter from vcfl […]

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

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