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.”

Advertisements

VarAFT

[PMID: 29860484] [Nucleic Acids Research]

VarAFT: a variant annotation and filtration system for human next generation sequencing data

“VarAFT is a multiplatform freely available software that allows the simultaneous annotation, filtration, and breadth and depth of coverage analysis of WES, WGS and targeted sequencing experiments from any sequencing platform. Its graphical user interface, various modules and unique features, such as pathogenicity predictions from UMD-Predictor and HSF, allow untrained users to rapidly highlight disease-causing mutations in multiple genetic scenarios.”

Heritability from EHR

[PMID: 29779949] [Cell]

Disease Heritability Inferred from Familial Relationships Reported in Medical Records

“We mined emergency contact data at three academic medical centers and identified 7.4 million familial relationships while maintaining patient privacy. Identified relationships were consistent with genetically derived relatedness. We used EHR data to compute heritability estimates for 500 disease phenotypes. Overall, estimates were consistent with the literature and between sites. Inconsistencies were indicative of limitations and opportunities unique to EHR research.”