LinkImpute

[…] merged using a custom perl script, preferentially keeping snps called by psti-ecot22i at overlapping sites, since those sites tended to have higher coverage., missing genotypes were imputed using linkimputer v0.9 (money et al., ) with global thresholds of 0.01 for minor allele frequency (maf) and 0.70 for missingness. we examined depths of 3–8 and selected a case for imputation with a max […]

[…] snp calling methods., genetic maps were constructed from 70% mcr, 50% mcr and 20% mcr tgbs (grl2) snp sets in the ibm rils with the same filtering described for segmentation using asmap (). linkimpute () was run with the default settings. snps imputed from linkimpute and unimputed snps for each mcr were imported into asmap () for map construction. rils with high similarity were detected […]

[…] reference genome (with chromosome-scale pseudomolecules), which is still not available for ryegrass. efficient, haplotype-independent imputation methods exist, such as those implemented in linkimpute (money et al., , ); however, such methods were developed for standard marker coding as counts of alleles, and so cannot be applied to pool allele-frequencies. the unavailability […]

[…] in ., genetic data were filtered using plink v1.07 (). the minor allele frequency threshold was set at 5% and the missingness by individual filter at 10%. missing genotypes were imputed using linkimpute v 1.1.1, a k-nearest neighbor imputation technique (). accuracy of the imputation was 0.966 using two nearest neighbors (k = 2) and 65 snps (l = 65). the final genotype set, after manual […]

[…] merged using a custom perl script, preferentially keeping snps called by psti-ecot22i at overlapping sites, since those sites tended to have higher coverage., missing genotypes were imputed using linkimputer v0.9 (money et al., ) with global thresholds of 0.01 for minor allele frequency (maf) and 0.70 for missingness. we examined depths of 3–8 and selected a case for imputation with a max […]

[…] deviations of the defined clusters. a total of 14,898 polymorphic snps were obtained. following filtering to remove snps with >50% missing data, the remaining 13,159 snps were imputed using linkimpute software with default parameters (money et al., ). after imputation, snps without position on the consensus map and snps with a minor allele frequency (maf) <5% in the recipient […]

[…] to perform genomic prediction, snps with a maf threshold of <0.01 were removed using plink, resulting in 4602 snps genotyped in 580 accessions. missing genotype data were then imputed using linkimpute with optimized values of 7 for parameter k and 23 for l, resulting in an estimated accuracy of 88.8%. genomic prediction was performed on all phenotypes using imputed data and the x.val […]