Порівняння методів

	Мережевий виклик варіантів	Виявлення варіантів
Галузь	Біоінформатика	Біоінформатика
Родина	Process / pipeline	Process / pipeline
Рік появи	2017–2018	2009–2010 (modern high-throughput era)
Автор методу	Erik Garrison, Paten lab (UCSC); Hannes Eggertsson, deCODE Genetics	Li et al. (SAMtools/bcftools, 2009); McKenna et al. (GATK, 2010)
Тип	Computational genomics pipeline	Computational genomics pipeline
Основоположне джерело	Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., Paten, B., & Durbin, R. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology, 36(9), 875–879.	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.
Інші назви	graph-genome variant calling, variation graph genotyping, vg-based variant calling, pangenome variant calling	SNP calling, genotyping from sequencing, mutation detection, variant detection
Пов'язані	6	6
Підсумок	Network-based (graph-genome) variant calling replaces the conventional single linear reference genome with a variation graph — a network in which nodes represent sequence segments and edges represent known alternative paths through the genome. Reads are mapped onto this graph, enabling detection of SNPs, indels, and structural variants with substantially lower reference bias than linear-reference pipelines. Key tools include the Variation Graph Toolkit (vg) and Graphtyper.	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.