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chevron_left Deletion detection Insertion detection Structural variant detection Duplication detection Transposable element prediction Inversion detection chevron_right
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VariationHunter specifications

Information


Unique identifier OMICS_00328
Name VariationHunter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format DIVET
Biological technology Illumina
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability No
Maintained No

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Publication for VariationHunter

VariationHunter in publications

 (10)
PMCID: 5826927
PMID: 29483503
DOI: 10.1038/s41467-018-03273-1

[…] aim to address these issues., existing structural variation discovery tools are based on the following general strategies: detection of variants using discordantly mapping paired-end reads (e.g., variationhunter, and hydra which report only the rough loci of structural variants but not their sequence content); detection of variants using split-read mappings (e.g., socrates); and detection […]

PMCID: 5305044
PMID: 28228978
DOI: 10.1080/2159256X.2017.1280116

[…] detection methods altogether. table 2. figure 1. , two of the earliest computational methods developed specifically for the detection of te insertions from next-generation sequence data are variationhunter and the program spanner, which was used for calling te insertions in the first phase of the 1kgp. subsequent phases of the 1kgp included additional refinement of next-generation […]

PMCID: 5115803
PMID: 27861560
DOI: 10.1371/journal.pone.0166721

[…] (in sam and vcf standard) to distinguish reads carrying different alleles, which is necessary for subsequent haplotype assembly. however, existing sv callers (e.g., breakdancer, modil, or variationhunter) cannot supply the information required to distinguish reads for sv or non-sv haplotypes, and the accuracies of reported svs and boundaries are unsatisfactory [, ]. therefore, […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] sequence insertions larger than the average insert size. several tools based on the detection of sv signatures from clusters of read-pairs have been reported in the literature including breakdancer, variationhunter, pemer, and gasv (chen et al., ; hormozdiari et al., , ; korbel et al., ; sindi et al., ). remarkably, pemer can be exploited for the identification of linked insertions (medvedev et […]

PMCID: 4408412
PMID: 25633377
DOI: 10.1093/molbev/msv017

[…] approaches need to be developed to efficiently screen nonhuman mammalian genomes for functional l1s, in order to verify results from genome sequencing. one strategy is to involve pipelines such as variationhunter (), tif () or retroseq () that are specifically developed to identify polymorphic transposable element insertions between individuals in a population to gather evidence […]


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VariationHunter institution(s)
School of Computing Science, Simon Fraser University, Burnaby, BC, Canada

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