Variant Calling Features
SNP and Variant Calling
Geneious Prime includes built-in variant callers for SNPs, indels, and larger structural variants. After aligning reads to a reference genome, the variant calling tool identifies positions where the reads differ from the reference. You can configure minimum coverage, minimum variant frequency, strand bias filtering, and quality thresholds directly from the GUI.
Variant Filtering with Genome View
The integrated Genome View lets you visually inspect variants in context. Each called variant is shown alongside the read pile-up, so you can immediately see whether a variant is supported by reads on both strands, whether it is near a homopolymer run, or whether coverage drops at that position. Variants can be filtered by frequency, coverage, quality, type (SNP/indel), and custom annotations.
Annotation and Impact Prediction
Variants are automatically annotated against the reference genome's feature annotations. Coding variants are classified as synonymous, non-synonymous (missense), or nonsense (stop-gain/loss). This lets you quickly prioritize variants that are likely to affect protein function.
Expression Analysis Features
Expression Level Quantification
For RNA-seq data, Geneious Prime quantifies expression levels as read counts, RPKM, FPKM, or TPM per feature. The quantification integrates with the alignment results, and expression values are exported as tables for downstream analysis.
PCA (Principal Component Analysis)
Geneious Prime includes a built-in PCA plot for exploring sample-level variation in expression data. PCA helps you identify batch effects, confirm that replicates cluster together, and explore sources of variation across your experimental groups before performing differential expression analysis.
Volcano Plots
Differential expression results are visualized using volcano plots, which display log2 fold-change on the X-axis and -log10(P value) on the Y-axis. Significantly differentially expressed genes appear in the upper corners of the plot. Genes can be selected interactively on the volcano plot to view their read counts in a bar chart.
Integrated Workflow
The power of Geneious Prime for variant calling and expression analysis lies in the fully integrated workflow. You can go from raw FASTQ files to annotated variant tables or differential expression results without leaving the application or switching between command-line tools. All intermediate results (alignments, coverage plots, variant tables) remain linked and interactive throughout the analysis.
Key advantage: Geneious Prime's visual genome browser lets you immediately validate computational variant calls against the raw read data, reducing false positives and improving confidence in reported variants without additional bioinformatics expertise.