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

bin+lib varlociraptor

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

33 stable releases

2.5.4 Jan 4, 2021
2.5.3 Nov 23, 2020
2.3.0 Sep 9, 2020
2.0.0 Jul 9, 2020
1.1.1 Jul 9, 2019

#52 in Science

Download history 8/week @ 2020-09-20 7/week @ 2020-09-27 55/week @ 2020-10-04 1/week @ 2020-10-11 10/week @ 2020-10-18 31/week @ 2020-10-25 13/week @ 2020-11-01 75/week @ 2020-11-08 31/week @ 2020-11-15 52/week @ 2020-11-22 38/week @ 2020-11-29 43/week @ 2020-12-06 1/week @ 2020-12-13 47/week @ 2021-01-03

108 downloads per month

GPL-3.0 license

540KB
12K 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 and indels in all length ranges (from small to structural) with a unified statistical model.
  • The statistical model entails all possible sources of uncertainty.
  • 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

  • Tumor-normal-calling, classifying variants as somatic in tumor, somatic in normal, germline, or absent.
  • Generic, grammar based calling, allowing to classify arbitrary scenarios.

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

Dependencies

~33MB
~704K SLoC