github.com/snakemake-workflows/dna-seq-varlociraptor ↗
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
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Contributors
5
Lines of Code
469
From
2020-01-17
To
2021-01-18
About snakemake-workflows/dna-seq-varlociraptor
This is a Snakemake workflow for detecting genetic variants in DNA sequencing data across diverse experimental scenarios. It leverages Varlociraptor, a unified statistical framework, to call both small variants like single nucleotide polymorphisms and indels, as well as large structural variants. The workflow handles complex study designs including tumor-normal pairs, multi-sample longitudinal cases with relapse samples, germline studies, family pedigrees, and population-level analyses.
The project is built in Python and designed for reproducible bioinformatics research through Snakemake's workflow automation system. By implementing a single statistical model across different variant-calling scenarios, the workflow reduces complexity and improves consistency compared to using separate tools for each study design. It integrates with the Snakemake Workflow Catalog for standardized deployment and documentation, making it accessible to researchers familiar with Snakemake-based genomics pipelines.