variant calling
Definition
Variant calling is the computational process of identifying genetic differences (variants) between a sequenced genome and a reference genome. These variants include single nucleotide polymorphisms (SNPs), insertions, deletions (indels), and structural variations. The process involves aligning sequencing reads to a reference genome, detecting positions where reads differ from the reference, and applying statistical algorithms to distinguish true genetic variants from sequencing errors. Variant calling is fundamental to genomics research, enabling identification of disease-causing mutations, pharmacogenomic markers, and population-level genetic diversity. Accuracy depends on sequencing depth, read quality, alignment algorithms, and variant calling software. The output is typically a VCF (Variant Call Format) file containing variant positions, genotypes, and quality scores.
Visualize variant calling in Nodes Bio
Researchers can visualize variant calling results as networks connecting variants to affected genes, proteins, and pathways. In Nodes Bio, create networks showing how identified variants impact protein-protein interactions, disrupt regulatory networks, or cluster within specific biological pathways. Link variants to phenotypes, diseases, and drug targets to understand functional consequences and identify potential therapeutic interventions through network-based analysis.
Visualization Ideas:
- Variant-to-gene-to-pathway networks showing functional impact of identified mutations
- Patient similarity networks based on shared variant profiles and phenotypes
- Variant-drug interaction networks mapping mutations to therapeutic responses and resistance mechanisms
Example Use Case
A cancer genomics team performs whole-exome sequencing on tumor samples from 50 patients with treatment-resistant melanoma. Through variant calling, they identify recurrent mutations in BRAF, NRAS, and novel variants in lesser-known genes. By visualizing these variants in a network with known drug targets and resistance pathways, they discover that patients with co-occurring mutations in specific DNA repair genes show distinct pathway dysregulation patterns, suggesting combination therapy approaches that could overcome resistance mechanisms.