An automated workflow for single nucleotide polymorphisms detection is developed. This is known as OVarFlow [1]. This workflow also helps in the identification of insertions and deletions.
OVarFlow provides a wide range of applications in sequence annotation of model and non-model organisms [1]. The workflow is based on GATK best practices. It makes the task of variant calling easy by reducing the computation time and resources.
A reference genome is provided as input in FASTA format along with reference annotation in a general feature format (.gff.gz). After that, second-generation sequencing data is provided in fastq format. Using this data, functionally annotated variants are generated. The workflow also consists of an extended workflow that generates variants by base quality score recalibration (BQSR).
OVarFlow is written in Python & Snakemake, and Bash languages and is available for Linux on GitLab.
For more information, read here.
References
- Bathke, J., Lühken, G. (2021). OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow. BMC Bioinformatics 22, 402.
