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Genetic Variation

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

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.

  • 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

Cutting-Edge Genetic Variation Analysis​​

Identify and analyze genetic variations within a population or a species

Genetic Variation

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.

Reliable Pipeline to Leverage Your Analysis

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.

genetic_variation_screenshot2_2023
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Dive in Genetic Variation: Our Module Highlights

Genome-Wide Association Analysis and Gene Set Analysis

After performing Variant Calling and filtering unreliable variants, you can use OmicsBox to perform GWAS and analyse the associations between your variants and a set of phenotypes.

The insights gathered using GWAS can be further enriched performing a Gene Set Analysis (GSA) of GWAS data using MAGMA. This analysis turns out to be a powerful tool that can unveil associations between genetic variants and phenotypes at a gene-set level.

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Why work with Genetic Variation Module?

From FASTQ to Insights

Fast and easy, obtain significant insights starting from FASTQ files with OmicsBox.

End-to-End Genetic Variation studies all in the same platform.

Versatile Data Handling and Integration

Gain a unified and complete dataset by integrating multiple VCF files, and ensure data integrity with efficient phasing and imputation.

Extract essential information from large VCF files to achieve faster and more accurate insights.

Advanced Analysis Made Easy

Understand individuals’ genetic composition and ancestry proportions within a population through guided Population Structure Analysis.

Obtain information about which genes and gene sets might be associated with different phenotypes with your GWAS data.

End-to-end genetic analysis workflow

From alignments to population structure analysis and Gene Set Analysis of GWAS results.
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