Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• RNA-seq (transcriptome sequencing) is a cost-effective alternative to whole-genome sequencing for variant identification.
• Existing variant callers struggle with RNA-seq data due to reads spanning intronic regions.

Purpose of the Study:

• To develop a software solution, Opossum, to pre-process RNA-seq reads for improved variant calling.
• To evaluate Opossum's performance in conjunction with established variant callers.

Main Methods:

• Opossum software was developed to pre-process RNA-seq reads.
• Opossum was tested with Platypus and GATK HaplotypeCaller variant callers.
• Performance was compared against the GATK Best Practices pipeline.

Main Results:

• Using Opossum with Platypus or GATK HaplotypeCaller maintained precision and improved SNP detection sensitivity.
• Opossum combined with Platypus significantly reduced run times compared to the GATK pipeline.

Conclusions:

• Opossum effectively addresses challenges in RNA-seq variant calling.
• The Opossum-Platypus combination offers a computationally efficient and sensitive approach for SNP detection from RNA-seq data.