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CCRaVAT specifications


Unique identifier OMICS_24943
Alternative name Case-Control Rare Variant Analysis Tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Eleftheria Zeggini

Publication for Case-Control Rare Variant Analysis Tool

CCRaVAT citations


A comprehensive evaluation of collapsing methods using simulated and real data: excellent annotation of functionality and large sample sizes required

Front Genet
PMCID: 4164031
PMID: 25309579
DOI: 10.3389/fgene.2014.00323

[…] tudy some of the given method features were not considered due to software limitations or great computational costs. In case of RVT2, covariates were not included in the analysis because the software CCRaVaT does not allow for this feature. Furthermore, for VT and PWST, only the quantitative phenotype was considered because calculations for the affection status were computationally intractable. Fo […]


Methodology for the analysis of rare genetic variation in genome wide association and re sequencing studies of complex human traits

Brief Funct Genomics
PMCID: 4168660
PMID: 24916163
DOI: 10.1093/bfgp/elu012
call_split See protocol

[…] ‘super-allele’ such that where if , and , otherwise. This collapsing technique has been implemented in a Fisher’s exact test for a 2 × 2 contingency table for dichotomous phenotypes in CAST [] and CCRaVAT [], and in an ANOVA framework for quantitative traits in QuTie []. The combined multivariate and collapsing method extends this approach to allow for simultaneous analysis of multiple super-al […]


Genes Contributing to Pain Sensitivity in the Normal Population: An Exome Sequencing Study

PLoS Genet
PMCID: 3527205
PMID: 23284290
DOI: 10.1371/journal.pgen.1003095

[…] ogous to traditional multivariate analysis on a binary trait simple threshold test: a case/control by subject on carriers with one or more variants having MAF<0.05. It is similar to the CAST method CCRaVAT (using Pearson test): collapsing method examining the accumulation of rare alleles using analysis of contingency tables. Like ARIEL, it is sensitive to linkage disequilibrium, however it evalu […]


Comparison of collapsing methods for the statistical analysis of rare variants

BMC Proc
PMCID: 3287839
PMID: 22373249
DOI: 10.1186/1753-6561-5-S9-S115
call_split See protocol

[…] version 2.12.0 []. The input data are further converted with GTOOL, version 0.5.0 [], into the SNPTEST format for running GRANVIL, version 0.4, which is an implementation of RVT1 [], and for running CCRaVAT [], an implementation of RVT2 []. GRANVIL and CCRaVAT are run with default values.Only genes with at least two variants are included. Furthermore, we exclude the 695 spuriously associated gene […]


Rare variant collapsing in conjunction with mean log p value and gradient boosting approaches applied to Genetic Analysis Workshop 17 data

BMC Proc
PMCID: 3287936
PMID: 22373203
DOI: 10.1186/1753-6561-5-S9-S94

[…] We use the collapsing method proposed by Li and Leal [] and Morris and Zeggini [] to identify possible variants among rare SNPs. For this analysis we use the CCRaVAT (Case-Control Rare Variant Analysis Tool) software package []. The collapsing method is as follows: first, we divide the markers into groups on the basis of predefined criteria (either genes o […]


Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis

Hum Genet
PMCID: 2978888
PMID: 20852893
DOI: 10.1007/s00439-010-0889-1
call_split See protocol

[…] st (or Fisher’s exact test where necessary). For regions attaining p < 10−4, we also permuted case/control status 100,000 times in order to assess significance by means of empirical p values. We used CCRaVAT software to carry out these analyses ( For the purposes of this study, variants with a MAF ≤0.05 were considered low frequency/rare a […]


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CCRaVAT institution(s)
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Wellcome Trust Sanger Institute, Hinxton, UK
CCRaVAT funding source(s)
Supported by the Wellcome Trust (WT088885/Z/09/Z and 079557MA).

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