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Development of Strategies for SNP Detection in RNA Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

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Figure 1. Analysis strategies and methods for RNA-seq SNP detection. This figure outlines the analysis strategies and methods used toidentify the best performing methods of RNA-seq SNP detection
Figure 2. Number of SNPs per method in RNA-seq data. Thisfigure displays the number of SNPs called for each of the 8 methodsused
Figure 3. Specificity and sensitivity of the SNP calls from RNA-seq data. This figure displays the specificity (A) and sensitivity (B) ofthe SNP calls for each of the 8 methods at a range of coverage depths.Solid lines represent calls made where duplicate reads had beenremoved pre-alignment and broken lines are calls generated whenduplicate reads are removed post-alignment.doi:10.1371/journal.pone.0058815.g003
Figure 5. Specificity and sensitivity of the SNP calls from RNA-seq data for all three samples

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