Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection [version 1; referees: 2 approved, 1 approved with reservations]

• Main Authors: Laura Oikkonen, Stefano Lise
• Format: Article
• Language: English
• Published: Wellcome 2017-01-01
• Series: Wellcome Open Research
• Subjects: Bioinformatics
• Online Access: https://wellcomeopenresearch.org/articles/2-6/v1

Identifying variants from RNA-seq (transcriptome sequencing) data is a cost-effective and versatile alternative to whole-genome sequencing. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller. In this work, we show that using Opossum in conjunction with either Platypus or GATK HaplotypeCaller maintains precision and improves the sensitivity for SNP detection compared to the GATK Best Practices pipeline. In addition, using it in combination with Platypus offers a substantial reduction in run times compared to the GATK pipeline so it is ideal when there are only limited time or computational resources available.