Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data
de Souza, V. B. C.; Jordan, B. T.; Tseng, E.; Nelson, E. A.; Hirschi, K. K.; Sheynkman, G. M.; Robinson, M. D.
Show abstract
Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms. Furthermore, there is opportunity to call variants directly from lrRNA-seq data. However, most state-of-the-art variant callers have been developed for genomic DNA. Here, there are two objectives: first, we perform a mini-benchmark on GATK, DeepVariant, Clair3, and NanoCaller primarily on PacBio Iso-Seq, data, but also on Nanopore and Illumina RNA-seq data; second, we propose a pipeline to process spliced-alignment files, making them suitable for variant calling with DNA-based callers. With such manipulations, high calling performance can be achieved using DeepVariant on Iso-seq data.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
Similar papers in this journal
- Kmerator Suite: design of specific k-mer signatures andautomatic metadata discovery in large RNA-Seq datasets. 95%
- Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing 94%
- Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery 94%
Similar papers in this journal
- LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants 95%
- OctopusV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis 95%
- Bayesian Estimation of Allele-Specific Expression in the Presence of Phasing Uncertainty 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.