varlociraptor

A Rust library for calling genomic variants using a latent variable model. This library is under active development. A preprint describing an early version of the model can be found here: https://doi.org/10.1101/121954.

Authors

Model

• Johannes Köster (strand bias, sampling probability, allele probabilities, FDR control, prior probabilities, grammar of variants, CNV calling)
• Louis Dijkstra (latent variable model)
• David Lähnemann (single cell whole genome amplification model, single cell & bulk joint calling model / event setup)
• Alexander Schönhuth (latent variable model, single cell whole genome amplification model, single cell & bulk joint calling model / event setup)

Implementation

• Johannes Köster (framework, software architecture, model, tumor-normal variant calling, generic variant calling, filtration, CNV calling)
• David Lähnemann (single cell variant calling, FDR on Event sets)

Supervision

• Supervision of David Lähnemann: Alice McHardy, Alexander Schönhuth, Johannes Köster

Affiliations during work on the project

• Life Sciences and Health group, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands: Louis Dijkstra, Johannes Köster, Alexander Schönhuth
• Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany: David Lähnemann, Alice McHardy
• Algorithms for reproducible bioinformatics lab, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Germany: Johannes Köster, David Lähnemann
• Department of Pediatric Oncology, Hematology, and Clinical Immunology, University Children’s Hospital, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany: David Lähnemann