Single Nucleotide Variant Calling Tools for RNA-Seq

Abstract

Dissecting the transcriptome is essential for understanding the functional element of genome and molecular constituents of cells and tissues, and also important for revealing the cancer mechanism. Highthroughput RNA sequencing (RNA-Seq) has enabled whole genome and transcriptome single nucleotide variant (SNV) discovery in cancer. In recent years, a number of SNV identification methods have been published from both public and commercial sources. Here we presented an overview and evaluation of these attempts on SNV calling. We defined a set of criteria and compared the performance of four tools (GATK, Samtools, VarScan and Array Studio) based on these criteria, and we further provided advices on lowering false positive mutation rate. 