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Deprecated: Implicit conversion from float 235.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Proc+Natl+Acad+Sci+U+S+A 2017 ; 114 (10): E1923-32 Nephropedia Template TP
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PEMapper and PECaller provide a simplified approach to whole-genome sequencing #MMPMID28223510
Johnston HR; Chopra P; Wingo TS; Patel V; Epstein MP; Mulle JG; Warren ST; Zwick ME; Cutler DJ; Morrow B; Emanuel B; McDonald-McGinn DM; Scherer S; Bassett A; Chow E; Vermeesch J; Swillen A; Gur R; Bearden C; Kates W; Shashi V; Simon T; Chopra P; Cubells J; Cutler DJ; Epstein MP; Johnston HR; Mulle J; Patel V; Warren ST; Wingo TS; Zwick ME; Campbell L; Repetto G; Vorstman J; Van Amelsvoort T; Eliez S; Philip N; Gothelf D; Van Den Bree M; Owen M; Murphy C; Murphy D; Garcia-Minaur S; Neine-Suner D; Murphy K; Armando M; Vicari S
Proc Natl Acad Sci U S A 2017[Mar]; 114 (10): E1923-32 PMID28223510show ga
PEMapper and PECaller are paired software programs that simplify mapping and variant calling for whole-genome datasets. Whole-genome sequencing data are fast becoming the most natural dataset for all genetic studies. Analysis tools for data at this scale are essential. This manuscript describes tools, which solve the challenges of data analysis at whole-genome scale, using an approach involving 16-mer mapping and SNP calling based on a Pólya?Eggenberger distribution for SNP genotypes. We show that our software package is faster (cheaper to run), uses much less disk space (cheaper to store results), requires no previous knowledge of existing genetic variation (easier to deploy to nonhuman species), and achieves calling results that are as good as Genome Analysis Toolkit best practices.