#variant #genomic #calling #model #scenario #approach #novel

bin+lib varlociraptor

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

109 stable releases (7 major)

8.4.8 May 27, 2024
8.4.6 Mar 27, 2024
8.4.2 Nov 9, 2023
8.3.0 Jun 28, 2023
1.1.1 Jul 9, 2019

#50 in Biology

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GPL-3.0 license

1MB
22K SLoC

Varlociraptor

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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

~44–59MB
~1M SLoC