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

## TL;DR

PanVC 3 is a new software tool that improves genotyping accuracy by reducing reference bias and better calling insertions and deletions.

## Contribution

PanVC 3 introduces a novel approach using founder sequences with known variants to reduce reference bias in genotyping.

## Key findings

- Using founder sequences with known variants reduces reference bias in genotyping.
- Precision of insertion and deletion calling is improved with PanVC 3.

## Abstract

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.

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.