Tag: Variant Calling

ALFRED

[PMID: 29973584] [Nature Communications]

Systematic discovery of germline cancer predisposition genes through the identification of somatic second hits

“a statistical method, ALFRED, that tests Knudson’s two-hit hypothesis to systematically identify CPGs (cancer predisposition genes) from cancer genome data.”

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BayesTyper

[PMID: 29915429] [Nature Genetics]

Accurate genotyping across variant classes and lengths using variant graphs

“a new method (BayesTyper) that uses exact alignment of read k-mers to a graph representation of the reference and variants to efficiently perform unbiased, probabilistic genotyping across the variation spectrum.”  The BayesTyper genotyping process occurs in two stages: 1) Generation of variant candidates (using other tools); 2) Genotyping based on variant candidates (using BayesTyper). As indicated, BayesTyper does not find candidate variants on its own.