wANNOVAR protocols

wANNOVAR specifications

Information


Unique identifier OMICS_00194
Name wANNOVAR
Interface Web user interface
Restrictions to use None
Input data A list of variants.
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Kai Wang <>

Publication for wANNOVAR

wANNOVAR IN pipelines

 (4)
2017
PMCID: 5412354
PMID: 28379183
DOI: 10.3390/ijms18040770

[…] previous genetic tests of the proband showed no duplication of pmp22., a total of 204 variants, comprising 162 snps and 42 indels, were called by haplotypecaller with confidence score ≥50. using wannovar, after filtering by allele frequency to exclude variants with allele frequency ≥0.05 in the 1000 genome project and exome aggregation consortium (exac) database, three exonic or splice-site […]

2017
PMCID: 5709977
PMID: 29191219
DOI: 10.1186/s13195-017-0317-z

[…] the burrows-wheeler aligner (illumina) [49] to the grch37/hg19 reference genome, and variant calling was performed with the genome analysis toolkit (gatk) [50]. variants were annotated using the wannovar web server [51, 52], and their phenotypic effects were evaluated using the american college of medical genetics and genomics standards and guidelines [53]., neurons growing on a 96-well […]

2014
PMCID: 4102922
PMID: 25034901
DOI: 10.1038/srep05737

[…] libraries were pooled and sequenced together in one run on the illumina miseq platform. subsequently, we used bwa-mem13 to align the sequencing reads, gatk software tool to call variants14, and the wannovar web server1118 to annotate variants detected from the sequencing data. on average, each sample had 4.6 million (range: 2.9–6.9) qc-passed reads, and 99.41% (range: 97.55% to 99.82%) […]

2014
PMCID: 4102922
PMID: 25034901
DOI: 10.1038/srep05737

[…] we examined the variant calls generated on these nine samples. on average, we identified 234 snvs per sample, with the vast majority being non-coding variants. based on variant annotation from the wannovar web server, these nine samples carried 4, 8, 3, 7, 4, 2, 7, 7 and 6 non-synonymous snvs, respectively. additionally, we identified a nonframeshift deletion from one control subject […]

wANNOVAR institution(s)
Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Psychiatry and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
wANNOVAR funding source(s)
Supported by start-up funds from the Zilkha Neurogenetic Institute and grant number HG006465 from NIH/NHGRI.

wANNOVAR review

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Liana Oliveira

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Web
It is very easy to use and gives very useful information on the variants. All you have to do is to upload a vcf file (or a list of variants) and it returns, by email, a csv file with the annotations. The limitation is that it only annotates and does not prioritize variants. It allows you to use Phenolyzer in the same submission, but I am not sure yet if Phenolyzer gene prioritization is efficient.