#genomic #variant #model #variable #variants #free #parameter

bin+lib varlociraptor

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

59 stable releases

4.5.0 Oct 7, 2021
4.4.2 Sep 14, 2021
4.1.1 Jul 22, 2021
3.5.0 Jul 2, 2021
1.1.1 Jul 9, 2019

#95 in Science

Download history 15/week @ 2021-06-30 37/week @ 2021-07-07 50/week @ 2021-07-14 18/week @ 2021-07-21 105/week @ 2021-07-28 68/week @ 2021-08-04 93/week @ 2021-08-11 7/week @ 2021-08-18 15/week @ 2021-08-25 27/week @ 2021-09-01 22/week @ 2021-09-08 27/week @ 2021-09-15 1/week @ 2021-09-22 79/week @ 2021-09-29 17/week @ 2021-10-06 82/week @ 2021-10-13

173 downloads per month

GPL-3.0 license

720KB
16K SLoC

Varlociraptor

Bioconda GitHub Workflow Status Codecov API docs Conventional Commits Gitpod Ready-to-Code

Varlociraptor implements a novel, unified fully uncertainty-aware approach to genomic variant calling in arbitrary scenarios.

Key features

  • Calls SNVs, MNVs, indels, inversions, duplications, replacements and breakends in all length ranges (from small to structural) with a unified statistical model.
  • The statistical model encompasses all possible sources of uncertainty and biases.
  • Resulting variant calls can be filtered by false discovery rate. No parameter tuning necessary.
  • Unbiased, maximum a posteriori allele frequency estimates are provided with each call.

Calling modes

  • Generic, grammar based configuration of the statistical model, allowing to classify arbitrary scenarios, from poplation genetics, to pedigrees, complex tumor scenarios and arbitrary combinations thereof.
  • Tumor-normal-calling, classifying variants as somatic in tumor, somatic in normal, germline, or absent.

For details, see the homepage: https://varlociraptor.github.io

Dependencies

~44MB
~1M SLoC