A survey of tools for variant analysis of next-generation genome sequencing data. Pabinger et al. 2013
Following last week”s variant caller themed FF post, I will present you a very great article about variant detection and annotation. The paper gives a great review of basically every aspect of NGS based variant detection from a whole NGS analysis workflow and available tools to specific problems (e.g. detection of somatic mutations).
My favourite part is Figure 2, which illustrates perfectly, that there is no perfect variant caller around, even for germline mutations. Each tool finds (and misses) a different set of variants.
Figure 2 from Pabinger et al. 2013: Venn diagrams showing the number of identified variants for tested germline (A), somatic (B), CNV (C) and exome CNV (D) tools. The depicted numbers in (A) and (B) report identified SNPs and INDELs.
