Phase 3: Variant annotation and prioritization
This phase serves to select those variants that are of particular interest, depending on the research problem at hand. The methods are specific to the problem, thus we do not elaborate on them, and only provide a list of some commonly used tools below:
- Generating variant and sample-level annotations, and performing many other exploratory and filtration analysis types: Hail 1
- Exploring and prioritizing genetic variation in the the context of human disease: GEMINI 2
- Mendelian disease linked variants: VAR-MD, KGGSeq, FamSeq 3.
- Predicting the deleteriousness of a non-synonymous single nucleotide variant: dbNSFP, HuVariome, Seattle-Seq, ANNOVAR, VAAST, snpEff
- Identifying variants within the regulatory regions: RegulomeDB 4
Bibliography
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hail-is/hail: Scalable genomic data analysis. at https://github.com/hail-is/hail ↩
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Paila, U., Chapman, B. A., Kirchner, R. & Quinlan, A. R. GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput. Biol. 9, e1003153 (2013). ↩
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Peng, G. et al. Rare variant detection using family-based sequencing analysis. Proc Natl Acad Sci USA 110, 3985–3990 (2013). ↩
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Boyle, A. P. et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 22, 1790–1797 (2012). ↩
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