| Autor: |
Bruce Budowle, Shakeel Jessa, Jianye Ge, Stephen D. Turner, Matthew Scholz, August E. Woerner, Meng Huang, V.P. Nagraj |
| Jazyk: |
angličtina |
| Rok vydání: |
2022 |
| Předmět: |
|
| Zdroj: |
F1000Research, Vol 11 (2022) |
| Druh dokumentu: |
article |
| ISSN: |
2046-1402 |
| DOI: |
10.12688/f1000research.122840.1 |
| Popis: |
Motivation: Genotyping error can impact downstream single nucleotide polymorphism (SNP)-based analyses. Simulating various modes and levels of error can help investigators better understand potential biases caused by miscalled genotypes. Methods: We have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missingness in variant call format (VCF) files. We demonstrate how vcferr could be used to address a research question by introducing varying levels of error of different type into a sample in a simulated pedigree, and assessed how kinship analysis degrades as a function of the kind and type of error. Software availability: vcferr is available for installation via PyPi (https://pypi.org/project/vcferr/) or conda (https://anaconda.org/bioconda/vcferr). The software is released under the MIT license with source code available on GitHub (https://github.com/signaturescience/vcferr) |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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