imputeqc is an R package and accompanied scripts to estimate the quality of imputation of genotypes that was made with fastPHASE and BEAGLE softwares. Any other tools that support *.inp fastPHASE or VCF files can be also considered. The package is based on masked data analysis.

1. Estimation of the error of gynotype imputation.

2. Optimization of the imputation model parameters, e.g., the number of haplotype clusters. The parameter can be further used for the search of signatures of selection with hapFLK test.

3. Testing different reference panels for imputation.

4. Benchmarking of different imputation softwares and strategies.

Run from R.

1. Make sure you have devtools package installed.

install.packages("devtools")

2. Install dependencies

install.packages("BiocManager")
BiocManager::install("VariantAnnotation")

3. Install imputeqc

devtools::install_github("inzilico/imputeqc", build_vignettes = TRUE)

Read a vignette How to Select the Number of Clusters for fastPHASE.

• On a local machine, the vignette can be accessed as follow:

browseVignettes("imputeqc")

• On remote machine, the vignette can be opened in the "Help" tab of RStudio:

vignette("k_selection")

MIT

Khvorykh GV, Khrunin AV. imputeqc: an R package for assessing imputation quality of genotypes and optimizing imputation parameters. BMC Bioinformatics. 2020;21(Suppl 12):304. Published 2020 Jul 24. doi:10.1186/s12859-020-03589-0. [pubmed], [pdf]

Gennady Khvorykh, a bioinformatician, inzilico.com

Interested in contributing to the project? Suggestions, questions, and comments are open! Feel free to drop me the message.