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<p>We develop a freely-available Python package Vardetector (<a href="https://github.com/julijselb/vardetector/tree/main/vardetector">https://github.com/julijselb/vardetector/tree/main/vardetector</a>) used for detecting DNA called mutations in aligned RNA reads. We benchmark it by comparing it to industry standard variant caller (GATK HaplotypeCaller; <i>r</i> = 0.88896/0.88859 (supporting-reads/all-reads)) and demonstrate the functionality by comparing two RNA-seq library preparation protocols for formalin fixed paraffin embedded (FFPE) tumor samples. One protocol relies on exome-capture and the other on ribosome-depletion (ribodepletion) chemistry. We call somatic mutations from DNA of tumor/normal samples of two individuals with non-small cell lung cancer and test the difference between the two protocols by quantifying all RNA reads (all-reads) and somatic mutation supporting RNA reads (supporting-reads) over the positions of the DNA-called mutations. We show that the ribodepletion protocol produces significantly higher number of all (<i>p</i> &lt; 0.001) and of supporting (<i>p</i> &lt; 0.001) reads over the mutations of interest. Moreover, the ribodepletion protocol produces significantly (<i>p</i> &lt; 0.001) wider breath of somatic mutation position coverage. The Vardetector software package and our results display a meaningful potential of the approach to improve neoantigen prioritisation pipelines.</p>

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Vardetector: a pure Python package to detect DNA called mutations in aligned RNA reads

  • 期刊论文

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  • 发表日期：

    2026年6月27日

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  • Julij Šelb,
  • Luka Dejanović,
  • Katja Mohorčič,
  • Matija Rijavec,
  • Mateja Marc Malovrh,
  • Helena Jakopič,
  • Urška Janžič,
  • Loredana Mrak,
  • Rok Sekirnik,
  • Remig Arnak,
  • Kristina Tina Šelb,
  • Igor Požek,
  • Jelka Pohar,
  • Nina Rupar,
  • Mitja Rot,
  • Anže Smole,
  • Izidor Kern,
  • Peter Korošec

摘要

We develop a freely-available Python package Vardetector (https://github.com/julijselb/vardetector/tree/main/vardetector) used for detecting DNA called mutations in aligned RNA reads. We benchmark it by comparing it to industry standard variant caller (GATK HaplotypeCaller; r = 0.88896/0.88859 (supporting-reads/all-reads)) and demonstrate the functionality by comparing two RNA-seq library preparation protocols for formalin fixed paraffin embedded (FFPE) tumor samples. One protocol relies on exome-capture and the other on ribosome-depletion (ribodepletion) chemistry. We call somatic mutations from DNA of tumor/normal samples of two individuals with non-small cell lung cancer and test the difference between the two protocols by quantifying all RNA reads (all-reads) and somatic mutation supporting RNA reads (supporting-reads) over the positions of the DNA-called mutations. We show that the ribodepletion protocol produces significantly higher number of all (p < 0.001) and of supporting (p < 0.001) reads over the mutations of interest. Moreover, the ribodepletion protocol produces significantly (p < 0.001) wider breath of somatic mutation position coverage. The Vardetector software package and our results display a meaningful potential of the approach to improve neoantigen prioritisation pipelines.