Use of VMT involves simple steps to integrate data from different source files (e.g. VCF, SAM/BAM, genotype data from ExomeCytoChip, phenotype, genotype and variant information files of arbitrary formats), performing variant annotations, and selecting potentially causal variants from single or multiple exomes based on several parameters, including but not limited to mode of inheritance, variant sharing among pedigree members, population minor allele frequency (MAF), functional annotation and prediction, and if available results from linkage mapping studies. The design of VMT makes it possible for users to download our established protocol in VMT syntax which is compact and human-readable, to make adjustments to adapt the protocol to their research projects without having knowledge in programming, and to complete the analysis by simply submitting the protocol to the VMT environment. VMT also maintains a mechanism to organize and browse various protocol implementations, which greatly enhances speed and reproducibility of work and facilitates collaborations in data analysis. VMT will be highly beneficial to clinicians and researchers who aim to identify disease-causal variants from NGS data but have minimal knowledge and experience in the use of Linux and programming languages, variant annotations and/or variant discovery in family data.
Please visit the [httpshttp://statgen.research.bcm.eduus/VMT Downloads] area to download VMT [httpshttp://statgen.research.bcm.eduus/VMT source code], [httpshttp://statgen.research.bcm.eduus/VMT tutorial/documentation] and [httpshttp://statgen.research.bcm.eduus/VMT example data].
=Installation=
To install VMT,
* Download [httpshttp://statgen.research.bcm.eduus/VMT source code]
* Unarchive the files
<code>tar -xf VMT-.tar.gz</code>
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VMT [httpshttp://statgen.research.bcm.eduus/VMT documentation] is available in PDF format. Please also download and unzip [httpshttp://statgen.research.bcm.eduus/VMT example data], to run examples in the documentation.