{"doi":"10.1101/2022.02.08.479579","title":"Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data","abstract":"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.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":302672,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9094,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":571095,"name":"Ben T. Jordan","orcid":"0000-0003-2268-5226","position":1,"is_corresponding":false},{"id":107640,"name":"Elizabeth Tseng","orcid":"0000-0002-1074-5095","position":2,"is_corresponding":false},{"id":558828,"name":"Elizabeth A. Nelson","orcid":"0000-0002-1570-1083","position":3,"is_corresponding":false},{"id":254784,"name":"Karen K. Hirschi","orcid":"0000-0001-7116-0130","position":4,"is_corresponding":false},{"id":106260,"name":"Gloria Sheynkman","orcid":"0000-0002-4223-9947","position":5,"is_corresponding":false},{"id":32458,"name":"Mark D. Robinson","orcid":"0000-0002-3048-5518","position":6,"is_corresponding":false},{"id":994594,"name":"Vladimir B. C. de Souza","orcid":"0000-0001-6187-0489","position":0,"is_corresponding":true}],"reference_count":29,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:32:16.279991Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}