RNAIndel: A tool to identify somatic indels from tumor RNA-seq data

It is a challenging task to discover somatic coding indels that are generated during the preparation of the PCR-based RNA-seq library. A new tool called RNAIndel [1] has been developed for this purpose.

RNAIndel predicts indels in RNA-seq data and classifies them as somatic, germline, and artifact indels. RNAIndel implements a biological effect in a machine learning framework and predicts somatic indels with around 88-100% accuracy. RNAIndel is composed of 31 features in total including a count of repeats, relative indel location, and so on.

RNAIndel takes the RNA-seq BAM file as input mapped by STAR software [2]. After reading the input file, all indels are annotated using RefSeq [3] isoforms followed by querying a custom germline database for exact and equivalent matches. Indels having greater than or equal to two reads are predicted and classifies as single-nucleotide (s-indel) and multi-nucleotide (m-indel). Finally, it generates output in the VCF file consisting of indel entries, supporting reads, predicted class, and probability.

For further details, read here.

References

1. Hagiwara, K., Ding, L., Edmonson, M. N., Rice, S. V., Newman, S., Easton, J., … & Zhang, J. (2020). RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. Bioinformatics, 36(5), 1382-1390.
2. Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., … & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21.
3. O’Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., … & Astashyn, A. (2016). Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic acids research, 44(D1), D733-D745.