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FARVAT specifications

Information


Unique identifier OMICS_08180
Name FARVAT
Alternative name FAmily-based Rare Variant Association Test
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Sungho Won

Publication for FAmily-based Rare Variant Association Test

FARVAT citations

 (7)
call_split

WISARD: workbench for integrated superfast association studies for related datasets

2018
BMC Med Genomics
PMCID: 5918457
PMID: 29697360
DOI: 10.1186/s12920-018-0345-y
call_split See protocol

[…] iable threshold (VT) method [], and SKAT [, ], etc. In particular, most of gene-level tests were limited to population-based samples, and few approaches available for family-based samples. PEDCMC [], FARVAT [], mFARVAT [], and FARVATx [] are implemented in WISARD. Furthermore, we provided new statistics, family-based VT and family-based SKAT-o. Both are denoted by famVT and cFARVAT-o in the remain […]

call_split

Evaluation of Gene Based Family Based Methods to Detect Novel Genes Associated With Familial Late Onset Alzheimer Disease

2018
Front Neurosci
PMCID: 5893779
PMID: 29670507
DOI: 10.3389/fnins.2018.00209
call_split See protocol

[…] ssion disequilibrium) from the following family-based packages: SKAT (Wu et al., ), FSKAT (Yan et al., ), GSKAT (Wang et al., ), RVGDT (He et al., ), EPACTS (http://genome.sph.umich.edu/wiki/EPACTS), FarVAT (Choi et al., ), PedGene (Schaid et al., ), RareIBD (Sul et al., ). Some of these software offer the option to run different gene-based algorithms; e.g., GSKAT, EPACTS, FarVAT or PedGene can ru […]

library_books

Comparing family based rare variant association tests for dichotomous phenotypes

2016
BMC Proc
PMCID: 5133528
PMID: 27980633
DOI: 10.1186/s12919-016-0027-8

[…] In this report, we evaluated several FBATs for detecting rare variants using GAW19 data. We found that FARVAT and PedGene usually provide similar statistical efficiency, and recommend the SKAT-O–type statistic provided by FARVAT because its power has been robust under various disease models. In additio […]

library_books

Prioritization of family member sequencing for the detection of rare variants

2016
BMC Proc
PMCID: 5133500
PMID: 27980641
DOI: 10.1186/s12919-016-0035-8

[…] e; however, the familial relationship between these potential controls and cases had not yet been taken into consideration. Family structure was determined by kinship coefficients calculated with the family-based rare variant association test (FARVAT) using pedigree data []. Controls who were unrelated to any case were excluded, as they were genetically uninformative. In addition, parent–child pai […]

call_split

Family based approaches: design, imputation, analysis, and beyond

2016
BMC Genet
PMCID: 4895701
PMID: 26866700
DOI: 10.1186/s12863-015-0318-5
call_split See protocol

[…] implementations were used by participants, including MONSTER (minimum p value optimized nuisance parameter score test extended to relatives) [], GEMMA (genome-wide efficient mixed-model analysis) [], FARVAT (family-based rare variant association test) VC [], Mendel [], and implementations derived as part of GAW19 participation []. Additionally, 2 contributions used a 2-stage approach to speed up t […]

call_split

Progress in methods for rare variant association

2016
BMC Genet
PMCID: 4895384
PMID: 26866487
DOI: 10.1186/s12863-015-0316-7
call_split See protocol

[…] quations–based–kernel association (GEE-KM) test [], an extended CMC test for pedigree data known as PedCMC [], a gene-level kernel and burden association tests for pedigree data (PedGene) [], and the family-based rare variant association test (FARVAT) []. Through simulation based on the 6 genes with the largest effects on both simulated SBP and DBP, they found that the FARVAT method based on optim […]

Citations

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FARVAT institution(s)
Interdisciplinary Program in bioinformatics, Seoul National University, Kwanak-ro Kwanak-gu, Seoul, Korea; Institute of Human Genetics, University of Bonn, Bonn, Germany; Harvard Medical School, Shattuck St, Boston, MA, USA; Center for Genomic Medicine, Brigham and Women's Hospital, Boston MA, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Institute for Genomic Mathematics, University of Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases, Bonn, Germany; Department of Statistics, Seoul National University, Kwanak-ro Kwanak-gu, Seoul, Korea; Department of Public Health Science, Seoul, Korea

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