Tackling reference bias in genotyping by using founder sequences with PanVC 3.
Ontology highlight
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.
SUBMITTER: Norri T
PROVIDER: S-EPMC10924279 | biostudies-literature | 2024
REPOSITORIES: biostudies-literature
Publications
Tackling reference bias in genotyping by using founder sequences with PanVC 3.
Bioinformatics advances 20240304 1
<h4>Summary</h4>Overcoming reference bias and calling insertions and deletions are major challenges in genotyping. We present <i>PanVC 3</i>, 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.<h4>Availability and implementation</h4>PanVC 3 and its source code are f ...[more]
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