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

bin+lib varlociraptor

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

27 stable releases

2.3.0 Sep 9, 2020
2.0.0 Jul 9, 2020
1.7.2 Jun 3, 2020
1.6.4 Mar 18, 2020
1.1.1 Jul 9, 2019

#61 in Science

Download history 64/week @ 2020-05-28 57/week @ 2020-06-04 2/week @ 2020-06-11 27/week @ 2020-06-18 42/week @ 2020-07-02 12/week @ 2020-07-09 44/week @ 2020-07-16 42/week @ 2020-07-23 22/week @ 2020-07-30 42/week @ 2020-08-06 54/week @ 2020-08-13 46/week @ 2020-08-20 59/week @ 2020-08-27 58/week @ 2020-09-03 8/week @ 2020-09-10

148 downloads per month

GPL-3.0 license

520KB
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

~29MB
~588K SLoC