Fig. 4

SNV and Indel specificity comparisons with other RNA-seq variant calling programs. STAR alignment was used for all except MAPRSeq_RVBoost, which used Tophat alignment. STAR alignment was pre-processed by PanMutsRx or Opossum and then variants were called by either GATK haplotype caller or Platypus. MAPRSeq_RVBoost variants were called by GATK unified genotyper. Default settings were used for variant calling and filtering. Specificity was calculated by TN/(TN + FP). TNs are the genomic positions with > = 10X coverage in RNA-seq calls but no variants present in DNA