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Module Genetic Variation

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The Genetic Variation Module allows to 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 detect variants in your alignment files: BCFtools mpileup and Freebayes. With OmicsBox, you not only receive a VCF file but also gain the ability to visualize various charts for quality control 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 Ensembl's Variant Effect Predictor. You only require the reference genome used in the Variant Calling step and the annotation file.o
  • 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 any variants from the VCF file that do not meet our quality standards across different fields.
  • 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 with either Genotype By Sequencing (GBS) data to simplify the genome being sequenced, or with Whole Genome Sequencing (WGS) to comprehensively identify variants across the entire genome.

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