{"id":107424,"date":"2023-04-24T19:10:20","date_gmt":"2023-04-24T23:10:20","guid":{"rendered":"https:\/\/med.virginia.edu\/cell-biology\/?p=107424"},"modified":"2026-05-22T17:01:14","modified_gmt":"2026-05-22T21:01:14","slug":"transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data","status":"publish","type":"post","link":"https:\/\/med.virginia.edu\/cell-biology\/2023\/04\/24\/transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data\/","title":{"rendered":"Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data"},"content":{"rendered":"

UVA Author:<\/strong> Karen Hirschi
\nCitation:<\/strong> de Souza VBC, Jordan BT, Tseng E, Nelson EA, Hirschi KK, Sheynkman G, Robinson MD. Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. Genome Biol 24, 91 (2023). https:\/\/doi.org\/10.1186\/s13059-023-02923-y<\/p>\n

DOI:<\/strong> https:\/\/doi.org\/10.1186\/s13059-023-02923-y<\/a>
\nPub-Med Number<\/strong>: <\/p>\n

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Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms. Furthermore, there is an 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.<\/p>\n<\/div>\n<\/div>\n<\/section>\n

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UVA Author: Karen Hirschi Citation: de Souza VBC, Jordan BT, Tseng E, Nelson EA, Hirschi KK, Sheynkman G, Robinson MD. Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. Genome Biol 24, 91 (2023). https:\/\/doi.org\/10.1186\/s13059-023-02923-y DOI: https:\/\/doi.org\/10.1186\/s13059-023-02923-y Pub-Med Number: Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including […]<\/p>\n","protected":false},"author":1740,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[13],"tags":[22],"class_list":["post-107424","post","type-post","status-publish","format-standard","hentry","category-featured-publications","tag-intranet"],"acf":false,"yoast_head":"\nTransformation of alignment files improves performance of variant callers for long-read RNA sequencing data - Department of Cell Biology<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/med.virginia.edu\/cell-biology\/2023\/04\/24\/transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data - Department of Cell Biology\" \/>\n<meta property=\"og:description\" content=\"UVA Author: Karen Hirschi Citation: de Souza VBC, Jordan BT, Tseng E, Nelson EA, Hirschi KK, Sheynkman G, Robinson MD. Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data. Genome Biol 24, 91 (2023). https:\/\/doi.org\/10.1186\/s13059-023-02923-y DOI: https:\/\/doi.org\/10.1186\/s13059-023-02923-y Pub-Med Number: Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/med.virginia.edu\/cell-biology\/2023\/04\/24\/transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data\/\" \/>\n<meta property=\"og:site_name\" content=\"Department of Cell Biology\" \/>\n<meta property=\"article:published_time\" content=\"2023-04-24T23:10:20+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2026-05-22T21:01:14+00:00\" \/>\n<meta name=\"author\" content=\"zkr7e@virginia.edu\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"zkr7e@virginia.edu\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/med.virginia.edu\\\/cell-biology\\\/2023\\\/04\\\/24\\\/transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/med.virginia.edu\\\/cell-biology\\\/2023\\\/04\\\/24\\\/transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data\\\/\"},\"author\":{\"name\":\"zkr7e@virginia.edu\",\"@id\":\"https:\\\/\\\/med.virginia.edu\\\/cell-biology\\\/#\\\/schema\\\/person\\\/b4929a1d4683383a392718e12166cd7f\"},\"headline\":\"Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data\",\"datePublished\":\"2023-04-24T23:10:20+00:00\",\"dateModified\":\"2026-05-22T21:01:14+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/med.virginia.edu\\\/cell-biology\\\/2023\\\/04\\\/24\\\/transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data\\\/\"},\"wordCount\":166,\"keywords\":[\"Intranet\"],\"articleSection\":[\"Featured Publications\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/med.virginia.edu\\\/cell-biology\\\/2023\\\/04\\\/24\\\/transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data\\\/\",\"url\":\"https:\\\/\\\/med.virginia.edu\\\/cell-biology\\\/2023\\\/04\\\/24\\\/transformation-of-alignment-files-improves-performance-of-variant-callers-for-long-read-rna-sequencing-data\\\/\",\"name\":\"Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data - 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