#variant #genome #varlociraptor

bin+lib varlociraptor

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

119 stable releases

8.7.1 Mar 5, 2025
8.6.1 Feb 14, 2025
8.5.1 Dec 9, 2024
8.4.12 Nov 28, 2024
1.1.1 Jul 9, 2019

#141 in Biology

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388 downloads per month
Used in predictosaurus

GPL-3.0 license

1MB
22K 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 population 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

~46–63MB
~1M SLoC