CCRaVAT pipeline

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


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  • person_outline Eleftheria Zeggini <>

Publication for Case-Control Rare Variant Analysis Tool

CCRaVAT IN pipelines

PMCID: 3287839
PMID: 22373249
DOI: 10.1186/1753-6561-5-S9-S115

[…] gtool, version 0.5.0 [11], into the snptest format for running granvil, version 0.4, which is an implementation of rvt1 [12], and for running ccravat [13], an implementation of rvt2 [5]. granvil and ccravat are run with default values., only genes with at least two variants are included. furthermore, we exclude the 695 spuriously associated genes that were identified by luedtke et al. [14]., […]

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

[…] scaling methods in plink., we use the collapsing method proposed by li and leal [4] and morris and zeggini [8] to identify possible variants among rare snps. for this analysis we use the ccravat (case-control rare variant analysis tool) software package [13]. the collapsing method is as follows: first, we divide the markers into groups on the basis of predefined criteria (either […]

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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