When imputation from lower density chips to HD chips is part of a weekly or monthly procedure for routinely processing genotypes, computing time may be an important factor in the choice of the imputation method.
To examine the distribution of TGS in the Gorkhas (Tibeto-Burman), we created a dataset of 100,000 virtual Gorkha (Tibeto-Burman) individuals from genotypic frequencies of the four polymorphisms obtained in the present study with randomly generated genotypes computed by online software GEMINI [28].
In addition, genotypes computed from single-cell sequences may allow not only the imputation of inherited risk variants by inferring SNP haplotypes, as for single-cell SNP-array data, but also genotyping of the inherited causal mutation directly.
We also estimated heritability using each of the methods 1 to 5. The adjusted means (p ) of the genotypes computed from the simulated data at the first stage were used as the phenotypic data in the second stage of the cross-validatory analyses.
As best guess genotypes (computed using Beagle, Browning and Yu 2009) were used in the analyses, we applied stringent post imputation quality thresholds on the imputation quality measure (i.e., we retained only SNPs with an imputation quality score above 0.8) and for the Hardy Weinberg equilibrium test (α = 1 × 10−4).
In our metric, the distance between sets of variants from two exome samples is computed without considering genotyping quality scores.
The threshold T1 defined as the minimum number of sequences per individual required for reliable genotyping was computed by Galan et al. [ 13] using a negative multinomial distribution (referred as T1Galan Negmult).
To identify these SNPs, only the breeds with the largest populations (Blonde d'Aquitaine, Charolais, Holstein, Limousine, Montbéliarde and Normande) were considered in order to avoid erroneous identification of errors due to the use of a low number of genotypes when computing the error rate for a SNP.
Alternatively, the approach by Baruch and Weller [ 8] involves several steps, where first, expected genotypes are computed for non-genotyped animals, then marker effects are estimated (using expected genotypes for non-genotyped animals), phenotypes are adjusted by known or expected marker effects, and finally polygenic EBVs are computed from adjusted phenotypes.
In RRGS_HYB, the molecular relationship matrix G of the genotyped individuals (all the Deli and La Mé and the n genotyped hybrid individuals) was computed using Deli and La Mé genotypes and hybrid gametotypes, taking the parental origin of marker alleles for hybrid individuals into account.
