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Kaviar specifications

Information


Unique identifier OMICS_29998
Name Kaviar
Alternative name Known VARiants
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 160204-Public
Maintained Yes

Documentation


Maintainer


  • person_outline Gustavo Glusman

Additional information


A second forum is available at https://groups.google.com/forum/#!forum/kaviar-discuss

Publication for Known VARiants

Kaviar citations

 (17)
library_books

Identification of missing variants by combining multiple analytic pipelines

2018
BMC Bioinformatics
PMCID: 5902939
PMID: 29661148
DOI: 10.1186/s12859-018-2151-0

[…] ion was similar among the three groups (Fig. , Additional file : Table S5). In addition, we compared variants from each group to public databases including dbSNP build 147, ESP, ClinVar, 1000G, ExAC, Kaviar, and HRC. We found that 61.98% of single-unique variants were recorded in public databases, suggesting that at least this proportion of these variants are likely true positives (Fig. , Addition […]

library_books

Germline mutations in candidate predisposition genes in individuals with cutaneous melanoma and at least two independent additional primary cancers

2018
PLoS One
PMCID: 5894988
PMID: 29641532
DOI: 10.1371/journal.pone.0194098

[…] tation [] and indels were detected with pindel [] and annotated to dbSNP144 by ANNOVAR []. Variants altering the coding sequence were selected that were present at a frequency of <1:100 (0.01) in the Kaviar aggregated control population [] […]

library_books

Systematic characterization of pan‐cancer mutation clusters

2018
Mol Syst Biol
PMCID: 5866917
PMID: 29572294
DOI: 10.15252/msb.20177974

[…] ver tool to the genome assembly build 37). This included variation data from the 1,000 genomes (Genomes Project C et al, ), dbSNP (Sherry et al, ), and other databases. Furthermore, we downloaded the Kaviar database (Glusman et al, ) as well as coordinates of genomic variants collected by the Exome Aggregation Consortium (release 1, a subset without the TCGA variants) (Lek et al, ) and assessed ov […]

library_books

Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework

2017
Genome Med
PMCID: 5735928
PMID: 29254494
DOI: 10.1186/s13073-017-0509-y

[…] y mentioned. Public databases are burgeoning with information about genetic variants in humans and in many model organisms. Resources such as dbSNP [], dbVar [], COSMIC [], cBioPortal [], UniProt [], Kaviar [], Clinvar [], HGMD [], ExAC, and gnomAD [] provide data on hundreds of millions of single-nucleotide variants (SNVs) and other types of genetic variations. Each database has a different focus […]

library_books

Identification of a novel genetic locus underlying tremor and dystonia

2017
Hum Genomics
PMCID: 5674688
PMID: 29110692
DOI: 10.1186/s40246-017-0123-5

[…] in variants that were present in public databases including NHLBI Exome Sequencing Project, 1000 genomes project (phase 3), Exome Aggregation Consortium (ExAC) (version 0.3.1), dbSNP (build 141), and Kaviar (Known VARiants) (September 2015) databases at an incidence of < 2%. Included variants were further selected based upon pathogenicity predicted by Polyphen2 (http://genetics.bwh.harvard.edu/pph […]

library_books

Evaluating somatic tumor mutation detection without matched normal samples

2017
Hum Genomics
PMCID: 5584341
PMID: 28870239
DOI: 10.1186/s40246-017-0118-2

[…] ntly, the pattern of putative mutation count decrease was similar in the TGS and WES cohorts: large initial decreases when removing 1000 genome variants; modest decreases after further excluding ESP, KAVIAR, and ExAC; and then large decreases after further filtering with a normal pool.As the WES cohort used TCGA data, matched normal samples were available for all tumors, enabling a direct comparis […]

Citations

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Kaviar institution(s)
Institute for Systems Biology, Seattle, WA, USA
Kaviar funding source(s)
Supported by the National Institutes of Health (RO1GM081083) and by the University of Luxembourg-Institute for Systems Biology Program.

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