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Listed here we describe Wham, benchmark it from a few other extensively applied SV identification tools–Lumpy, Delly and SoftSearch–and exhibit Wham’s capacity to identify and associate SVs with phenotypes using facts from humans, domestic pigeons, and vaccinia virus. Wham and all related software are coated under the MIT License and may be freely downloaded from github (), with documentation on the wiki (). For Neighborhood aid make sure you publish questions to .
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For a detailed description with the datasets utilized for the following analyses and computer software versions begin to see the Supporting data.
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We chose to benchmark Delly, Lumpy and SoftSearch due to the fact all 3 tools website can detect many sorts of SVs, are extensively made use of, and therefore are simple to put in and run directly from BAM data files. Lumpy also presents a point of reference from GASVPro and Pindel, as it's presently been benchmarked versus these applications beneath matched simulation circumstances [10,39]. We applied a Formerly printed interval measurement, (locations outlined by 25 bp up- and downstream of every simulated variant breakpoint) as “fact intervals” to find out legitimate beneficial phone calls, Except if not mentioned [14]. A SV is taken into account a real positive provided that the two with the referred to as breakpoints lie in a “real truth interval.” For certain facts regarding the simulations see Supporting Information and facts.
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