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Siccuracy: An R-package for executing genotype imputation strategy simulations with AlphaImpute

https://doi.org/10.1101/236760
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/gepi.20533openalex-snapshot
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
inferredcites →https://doi.org/10.1007/978-3-642-00727-9_29openalex-snapshot
cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models
inferredcites →https://doi.org/10.1017/s1751731114001803openalex-snapshot
Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications
inferredcites →https://doi.org/10.1038/ncomms10460openalex-snapshot
Complex disease and phenotype mapping in the domestic dog
inferredcites →https://doi.org/10.1038/ng786openalex-snapshot
Merlin—rapid analysis of dense genetic maps using sparse gene flow trees
inferredcites →https://doi.org/10.1038/nmeth.1785openalex-snapshot
A linear complexity phasing method for thousands of genomes
inferredcites →https://doi.org/10.1080/00221309809595548openalex-snapshot
Averaging Correlations: Expected Values and Bias in Combined Pearsonrs and Fisher'szTransformations
inferredcites →https://doi.org/10.1086/319501openalex-snapshot
A New Statistical Method for Haplotype Reconstruction from Population Data
inferredcites →https://doi.org/10.1086/502802openalex-snapshot
A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase
inferredcites →https://doi.org/10.1086/521987openalex-snapshot
Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1101/041277openalex-snapshot
VcfR: a package to manipulate and visualize VCF format data in R
inferredcites →https://doi.org/10.1101/gr.154831.113openalex-snapshot
Estimating and interpreting F ST : The impact of rare variants
inferredcites →https://doi.org/10.1111/1755-0998.12549openalex-snapshot
vcfr : a package to manipulate and visualize variant call format data in R
inferredcites →https://doi.org/10.1111/age.12677openalex-snapshot
Accuracy of genotype imputation in Labrador Retrievers
inferredcites →https://doi.org/10.1177/1536867x0800800307openalex-snapshot
Speaking Stata: Correlation with Confidence, or Fisher's z revisited
inferredcites →https://doi.org/10.1186/1297-9686-43-12openalex-snapshot
A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes
inferredcites →https://doi.org/10.1186/1297-9686-44-9openalex-snapshot
A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation
inferredcites →https://doi.org/10.1186/s12711-015-0102-zopenalex-snapshot
Potential of genotyping-by-sequencing for genomic selection in livestock populations
inferredcites →https://doi.org/10.1186/s12711-017-0300-yopenalex-snapshot
A hybrid method for the imputation of genomic data in livestock populations
inferredcites →https://doi.org/10.1186/s12863-014-0088-5openalex-snapshot
Impact of pre-imputation SNP-filtering on genotype imputation results
inferredcites →https://doi.org/10.1186/s12863-015-0248-2openalex-snapshot
Impact of genetic similarity on imputation accuracy
inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot
Second-generation PLINK: rising to the challenge of larger and richer datasets
inferredcites →https://doi.org/10.1371/journal.pbio.1001745openalex-snapshot
Best Practices for Scientific Computing
inferredcites →https://doi.org/10.1371/journal.pcbi.1005510openalex-snapshot
Good enough practices in scientific computing
inferredcites →https://doi.org/10.1371/journal.pgen.1000529openalex-snapshot
A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies
inferredcites →https://doi.org/10.1371/journal.pone.0009697openalex-snapshot
A New Statistic to Evaluate Imputation Reliability
inferredcites →https://doi.org/10.2135/cropsci2011.07.0358openalex-snapshot
Factors Affecting the Accuracy of Genotype Imputation in Populations from Several Maize Breeding Programs
inferredcites →https://doi.org/10.2135/cropsci2016.06.0526openalex-snapshot
Prospects for Cost‐Effective Genomic Selection via Accurate Within‐Family Imputation
inferredcites →https://doi.org/10.2307/1266577openalex-snapshot
Note on a Method for Calculating Corrected Sums of Squares and Products
inferredcites →https://doi.org/10.2527/jas.2013-6270openalex-snapshot
Practical implementation of cost-effective genomic selection in commercial pig breeding using imputation1
inferredcites →https://doi.org/10.3168/jds.2011-4490openalex-snapshot
Imputation of genotypes with low-density chips and its effect on reliability of direct genomic values in Dutch Holstein cattle
inferredcites →https://doi.org/10.3168/jds.2011-5019openalex-snapshot
Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels
inferredcites →https://doi.org/10.3168/jds.2012-6316openalex-snapshot
Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
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