Genetic Variation Module

Genetic VARIATION

Fast Variant Calling, Variant Filtering, Model & Non-Model Variant Annotation, GWAS, and more.

Identify and analyze genetic variations within a population or a species. Cutting-Edge Genetic Variation Analysis.

Fast Variant Calling

Choose between two of the best algorithms to find variants in your alignment files: BCFtools mpileup and Freebayes. Using OmicsBox, not only you will receive a VCF file, but also you will be able to visualize different charts to control the quality of your results.

Model & Non-Model Variant Annotation

Gather information about the coding and genetic consequences of all the variants included in a VCF file with the Variant Effect Predictor of Ensembl. You will only need the reference genome used in the Variant Calling step and the annotation file.

End-to-end Analysis

Create your VCF files with a Variant Calling algorithm, merge or extract information, and filter your VCF files. Then, you will be able to phase and impute your variants and perform a downstream analysis such as GWAS or Population Structure Analysis.

Variant Filtering

Remove those variants that have low quality according to your own standards regarding different fields in the VCF file.

Guided Genome-Wide Association Studies

Associate variants to different quantitative traits using GAPIT3 R package in a guided and easy way.

Supports GBS and WGS data

All these methods can be used both with Genotype By Sequencing (GBS) data if you seek to reduce the complexity of the genome to be sequenced, or Whole Genome Sequencing (WGS), if you want to thoroughly find variants across the entire genome.

Complete Feature List

Fast Variant Calling with BCFtools and FreeBayes
Variant Filtering
Variant Annotation with Variant Effect Predictor (VEP)
Guided Genome Wide Association Study
Supports GBS and WGS data
Functional Analysis of GWAS Results with MAGMA
Variant Calling Option for Mixed-ploidy in Freebayes
Merge and Extract VCF Files
Population Structure Analysis with ADMIXTURE
Imputation and Phasing with Beagle
Filtering Filtering for GBS data via dDocent Pipeline

The Genetic Variation Module allows for performing variant calling, filtering, and annotation, as well as associating genetic variations with a particular trait or disease via genome-wide association studies.

The module offers two different analysis strategies for variant calling and filtering based on the popular tools, BCFtools and FreeBayes. Many options are available to adjust the analysis to specific methodologies (e.g GBS vs WGS) or requirements (level of ploidy, genome coverage, presence of repetitive regions, etc.). The resulting VCF file can then be annotated using the Variant Effect Predictor from Ensembl.

This combination of tools has been shown to outperform alternative pipelines in several recent review studies (e.g. Nature Sci. Rep. 12, 11331 (2022)). Finally, the module also allows for the execution of guided genome-wide association studies (GWAS) to identify genetic variations associated with a particular trait.

Workflow

Benchmark

Soybean dataset

23 SAMPLES

0 GB

GBS vs. WGS ACCURACY

1 %

Total Execution

1 min