DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark

CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data

MOTIVATION Several algorithms exist for detecting copy number variants (CNVs) from human exome sequencing read depth, but previous tools have not been well suited for large population studies on the order of tens or hundreds of thousands of exomes. Their limitations include being difficult to integrate into automated variant-calling pipelines and being ill-suited for detecting common variants. ...

Scalable SDE Filtering and Inference with Apache Spark

In this paper, we consider the problem of Bayesian filtering and inference for time series data modeled as noisy, discrete-time observations of a stochastic differential equation (SDE) with undetermined parameters. We develop a Metropolis algorithm to sample from the high-dimensional joint posterior density of all SDE parameters and state time series. Our approach relies on an innovative densit...

Genome analysis CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data

Motivation: Several algorithms exist for detecting copy number variants (CNVs) from human exome sequencing read depth, but previous tools have not been well suited for large population studies on the order of tens or hundreds of thousands of exomes. Their limitations include being difficult to integrate into automated variant-calling pipelines and being ill-suited for detecting common variants....

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

MOTIVATION Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to con...

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