Process / pipelineBioinformatics / omics
Variant Calling — Genomic Variant Calling
Variant calling is the computational process of identifying positions in a sequenced genome that differ from a reference sequence — including single nucleotide polymorphisms (SNPs), small insertions and deletions (indels), and structural variants. It transforms aligned sequencing reads into an interpretable catalogue of genetic differences, forming the foundation for population genetics, disease-gene discovery, and clinical genomics applications.
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Sources
- McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., ... & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303. DOI: 10.1101/gr.107524.110 ↗
- Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078–2079. DOI: 10.1093/bioinformatics/btp352 ↗
Related methods
Referenced by
Bayesian ChIP-seq peak callingBayesian Copy Number Variation AnalysisBayesian Proteomics AnalysisBayesian RNA-seq differential expressionBayesian Sequence AlignmentBayesian Variant CallingChIP-seq Peak CallingCopy Number Variation AnalysisDifferential ChIP-seq peak callingGenome-wide association studyMachine learning-assisted ChIP-seq peak callingMachine learning-assisted copy number variation analysisNetwork-based copy number variation analysisNetwork-based Phylogenetic AnalysisNetwork-based variant callingPhylogenetic AnalysisRNA-seq Differential ExpressionSequence AlignmentSingle-cell Copy Number Variation AnalysisSingle-cell Phylogenetic AnalysisTime-series copy number variation analysisTime-series phylogenetic analysis