Varlociraptor

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