Biology subjects

Woerner, A. E.

Publications and source records attributed to Woerner, A. E..

2 recordsLinked to original sources

bioRxiv2022

vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework

MotivationGenotyping error can impact downstream SNP-based analyses. Simulating various modes and and levels of error can help investigators better understand potential biases caused by miscalled genotypes. ResultsWe have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missigness in 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 kind and type of error. Software Availabilityvcferr 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).

bioinformatics↗

bioRxiv2021

skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation

MotivationSNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream processing and manipulation. A dedicated software package that consistently and intuitively implements this analysis functionality is needed. ResultsHere we present the skater R package for SNP-based kinship analysis, testing, and evaluation with R. The skater package contains a suite of well-documented tools for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing IBD segment data. AvailabilityThe skater package is implemented as an R package and is released under the MIT license at https://github.com/signaturescience/skater. Documentation is available at https://signaturescience.github.io/skater.

bioinformatics↗