Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data.

ABSTRACT: The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and widespread use of this method for many research questions, ranging from unraveling the genetic basis of complex traits, to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies have determined, for example, the influence of sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated. Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools, leading to characteristic false positives in genome-wide scans. The problem of false positives was particularly pronounced wh

SUBMITTER: Kofler R 

PROVIDER: S-EPMC5100849 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature