vipR statistics

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Citations per year

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vipR specifications

Information


Unique identifier OMICS_00081
Name vipR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for vipR

vipR in pipeline

2017
PMCID: 5295625
PMID: 28179981
DOI: 10.1016/j.csbj.2017.01.002

[…] on bwa alignments the pipeline reporting the smallest number of snps (294) and vipr on bowtie2 alignments the pipeline reporting the largest number (4354) (a). the average number of indels was 80. vipr and snver were not able to detect any indel and varscan detected indels only from bowtie2 alignments., merging the variants predicted by the different pipelines, a raw dataset of 7925 variants […]


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vipR in publications

 (4)
PMCID: 5256917
PMID: 28114305
DOI: 10.1371/journal.pone.0170222

[…] quality than the rest, the average coverage per individual was 30x., in order to distinguish true calls from sequencing error, three different calling algorithms specific for pooled data were used (vipr [], snver [] and syzygy []). vipr was less sensitive than the other two algorithms and it called a much smaller number of variants, 39,211 snps and 459 deletions, compared to 62,506 snps […]

PMCID: 5295625
PMID: 28179981
DOI: 10.1016/j.csbj.2017.01.002

[…] aligner (bwa) with 7 variant discovery programs: freebayes , the genome analysis toolkit (gatk) , the next generation sequencing experience platform (ngsep) , samtools , snver , varscan and vipr . from these tools, snver and vipr were particularly designed to identify variation in pools. because freebayes and gatk presented problems or were not compatible with bowtie2 alignments, […]

PMCID: 3742761
PMID: 23967202
DOI: 10.1371/journal.pone.0071381

[…] in the early-onset group vs. late-detected group was 54∶22 for gjb2, 7∶1 for pcdh15, 8∶3 for slc26a4, 18∶2 for tecta, and 3∶5 for tmprss3., comparison data between the current algorithm and vipr, which is widely used for pooled sample analysis due to its higher specificity in mutation detection compared to other programs for pooled samples, is shown in . vipr is unable to detect […]

PMCID: 3712998
PMID: 23874702
DOI: 10.1371/journal.pone.0068645

[…] first run and grch37/hg19 for the second run) allowing a maximum of four mismatches. single nucleotide variant (snv) calling and annotation steps were performed as described in quast et al. using vipr and annovar . prerequisite for the inclusion into the variant calling procedure was that the coverage at a given base position in each pool had to be at least 5,000. thus in the first run 81.4% […]


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vipR institution(s)
Department of Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany

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