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Filtering and Annotation of Variants That Are Rare (FAVR)

ABSTRACT:

The project developed a suite of new methods (FAVR) designed to assist the shortlisting of genetic variants under a rare variant-phenotype/disease model. The methods were designed to work with commonly used massively parallel sequencing analysis pipelines, such as the GATK or ANNOVAR, and have been made publically available as a suite of software tools (https://github.com/bjpop/favr). The FAVR methods use signatures in comparator sequence alignment files to facilitate the filtering of mapping artifacts and common genetic variants, and annotation of genetic variants based on evidence of co-occurrence in individuals. As relevant, FAVR methods can also be used to filter out artifacts derived from imbalanced paired-end sequencing.

Pope et al., BMC Bioinformatics, accepted Dec 2012.

PROVIDER: phs000601.v1.p1 | EGA |

REPOSITORIES: EGA

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FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets.

Pope Bernard J BJ Nguyen-Dumont Tú T Odefrey Fabrice F Hammet Fleur F Bell Russell R Tao Kayoko K Tavtigian Sean V SV Goldgar David E DE Lonie Andrew A Southey Melissa C MC Park Daniel J DJ

BMC bioinformatics 20130225

<h4>Background</h4>Characterising genetic diversity through the analysis of massively parallel sequencing (MPS) data offers enormous potential to significantly improve our understanding of the genetic basis for observed phenotypes, including predisposition to and progression of complex human disease. Great challenges remain in resolving genetic variants that are genuine from the millions of artefactual signals.<h4>Results</h4>FAVR is a suite of new methods designed to work with commonly used MPS ...[more]

PMID: 23441864

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