Tackling reference bias in genotyping by using founder sequences with PanVC 3

Tuukka Norri; Veli Mäkinen

doi:10.1093/bioadv/vbae027

Tackling reference bias in genotyping by using founder sequences with PanVC 3

Bioinform Adv. 2024 Mar 4;4(1):vbae027. doi: 10.1093/bioadv/vbae027. eCollection 2024.

Authors

Tuukka Norri¹, Veli Mäkinen²

Affiliations

¹ Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland.
² Department of Computer Science, University of Helsinki, FI-00014 Helsinki, Finland.

Abstract

Summary: Overcoming reference bias and calling insertions and deletions are major challenges in genotyping. We present PanVC 3, a set of software that can be utilized as part of various variant calling workflows. We show that, by incorporating known genetic variants to a set of founder sequences to which reads are aligned, reference bias is reduced and precision of calling insertions and deletions is improved.

Availability and implementation: PanVC 3 and its source code are freely available at https://github.com/tsnorri/panvc3 and at https://anaconda.org/tsnorri/panvc3 under the MIT licence. The experiment scripts are available at https://github.com/algbio/panvc3-experiments.