• Lisle E Mose, Charles M Perou, and Joel S Parker.
• Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
• Bioinformatics. 2019 Sep 1; 35 (17): 2966-2973.

MotivationGenomic variant detection from next-generation sequencing has become established as an extremely important component of research and clinical diagnoses in both cancer and Mendelian disorders. Insertions and deletions (indels) are a common source of variation and can frequently impact functionality, thus making their detection vitally important. While substantial effort has gone into detecting indels from DNA, there is still opportunity for improvement. Further, detection of indels from RNA-Seq data has largely been an afterthought and offers another critical area for variant detection.ResultsWe present here ABRA2, a redesign of the original ABRA implementation that offers support for realignment of both RNA and DNA short reads. The process results in improved accuracy and scalability including support for human whole genomes. Results demonstrate substantial improvement in indel detection for a variety of data types, including those that were not previously supported by ABRA. Further, ABRA2 results in broad improvements to variant calling accuracy across a wide range of post-processing workflows including whole genomes, targeted exomes and transcriptome sequencing.Availability And ImplementationABRA2 is implemented in a combination of Java and C/C++ and is freely available to all from: https://github.com/mozack/abra2.Supplementary InformationSupplementary data are available at Bioinformatics online.© The Author(s) 2019. Published by Oxford University Press.

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