OVarFlow - an Open source Variant calling workFlow
Description
OVarFlow is an Open source Variant calling workflow for the discovery of SNVs (single nucleotide variants) and indels (insertions and deletions) utilizing short read next generation sequencing data. It is based upon the Genome Analysis Toolkit 4 (GATK) and the GATK Best Practice Workflow for "Germline short variant discovery (SNPs + Indels)". However the original Best Practice Workflow is intended for the evaluation of human short read sequencing data. OVarFlow has been designed to be broadly applicable for model as well as non-model diploid organisms. To guarantee long-term usability the workflow and all its required components have been bundled within a Singularity container, that is offered for download.
Source code is available at: https://gitlab.com/computational-biology/ovarflow
Documentation is available at: https://ovarflow.readthedocs.io/en/latest/
Licensing:
OVarFlow is licensed under GPLv3.0. Other licenses can apply to the used software components, e.g. Snakemake (MIT License), GATK (Apache License, Version 2.0) or Conda (3-clause BSD License).
Files
Files
(1.7 GB)
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md5:cb33c452da49f642db9627b66025c185
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md5:681626accd24c632b07c83fd0788b218
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732.8 MB | Download |