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

bin+lib varlociraptor

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

50 stable releases

new 4.1.1 Jul 22, 2021
3.5.0 Jul 2, 2021
2.6.5 Mar 19, 2021
2.5.3 Nov 23, 2020
1.1.1 Jul 9, 2019

#81 in Science

Download history 76/week @ 2021-04-03 63/week @ 2021-04-10 124/week @ 2021-04-17 11/week @ 2021-04-24 62/week @ 2021-05-01 4/week @ 2021-05-08 77/week @ 2021-05-15 33/week @ 2021-05-22 4/week @ 2021-05-29 47/week @ 2021-06-05 1/week @ 2021-06-19 10/week @ 2021-06-26 35/week @ 2021-07-03 7/week @ 2021-07-10 65/week @ 2021-07-17

115 downloads per month

GPL-3.0 license

685KB
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

~43MB
~1M SLoC