Salīdzināt metodes

	Tīklā balstīta variantu izsaukšana	Beiziešu variantu izsaukšana
Nozare	Bioinformātika	Bioinformātika
Saime	Process / pipeline	Process / pipeline
Izcelsmes gads	2017–2018	2010 (GATK framework); Bayesian genotyping principles preceded by Samtools/MAQ ~2008–2009
Autors	Erik Garrison, Paten lab (UCSC); Hannes Eggertsson, deCODE Genetics	Mark DePristo, Eric Banks, and the Broad Institute GATK team
Tips	Computational genomics pipeline	Probabilistic genomic inference pipeline
Pirmavots	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.
Citi nosaukumi	graph-genome variant calling, variation graph genotyping, vg-based variant calling, pangenome variant calling	Bayesian genotyping, probabilistic variant calling, GATK HaplotypeCaller, Bayesian SNP/indel detection
Saistītās	6	6
Kopsavilkums	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.	Bayesian variant calling is a computational pipeline that uses probabilistic inference to identify single-nucleotide polymorphisms (SNPs), insertions, and deletions in a genome by treating sequencing data as evidence and computing posterior probabilities over candidate genotypes. Unlike deterministic threshold-based callers, Bayesian approaches explicitly model sequencing error, mapping uncertainty, and prior genotype frequencies to produce calibrated genotype likelihoods that can be used for downstream filtering and association testing.