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使用PanVC 3的奠基者序列解决基因分型中的参考偏差问题。

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

作者信息

Norri Tuukka, Mäkinen Veli

机构信息

Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland.

Department of Computer Science, University of Helsinki, FI-00014 Helsinki, Finland.

出版信息

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

DOI:10.1093/bioadv/vbae027
PMID:38464975
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10924279/
Abstract

SUMMARY

Overcoming reference bias and calling insertions and deletions are major challenges in genotyping. We present , 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.

摘要

摘要

克服参考偏差以及识别插入和缺失是基因分型中的主要挑战。我们展示了一套软件，可作为各种变异识别工作流程的一部分使用。我们表明，通过将已知遗传变异整合到一组供体序列（reads与之比对的序列）中，参考偏差得以减少，识别插入和缺失的精度得以提高。

可用性与实现方式

PanVC 3及其源代码可在https://github.com/tsnorri/panvc3和https://anaconda.org/tsnorri/panvc3上根据MIT许可免费获取。实验脚本可在https://github.com/algbio/panvc3-experiments获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/d65cc360176f/vbae027f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/3179baef722a/vbae027f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/97db26c61094/vbae027f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/f3a5a9b42ce7/vbae027f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/ef1b529063c6/vbae027f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/f4008991c546/vbae027f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/d65cc360176f/vbae027f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/3179baef722a/vbae027f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/97db26c61094/vbae027f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/f3a5a9b42ce7/vbae027f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/ef1b529063c6/vbae027f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/f4008991c546/vbae027f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f5fe/10924279/d65cc360176f/vbae027f6.jpg

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