#model #variant #variables #calling #cell #events #genomic

libprosic

A library for calling of genomic variants using a latent variable model

10 releases (6 breaking)

Uses old Rust 2015

0.7.3 Dec 11, 2018
0.7.2 Nov 27, 2018
0.6.0 Jan 12, 2018
0.5.0 Nov 17, 2017
0.1.0 Nov 2, 2016

#207 in Biology

GPL-3.0 license

240KB
5K SLoC

libprosic

Travis API docs Crates.io Commitizen friendly

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 (sampling probability, indel allele probabilities, FDR control, prior probabilities)
  • 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)
  • David Lähnemann (single cell variant calling, FDR on Event sets) with strong support from Johannes Köster

Supervision

Affiliations

Affiliations during work on the project:

Dependencies

~22MB
~418K SLoC