Sentence examples for based on called genotypes from inspiring English sources

First, we proposed models based on called genotypes only circumventing imputation.

However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty.

The average gains in prediction accuracy varied greatly across traits and imputation methods, and in some cases methods that use imputed genotypes or inferred haplotypes were outperformed by methods based on called genotypes only.

We also called genotypes based on the maximum GLs and applied the genotype-based ML method from Choi et al. (2009) and PLINK (Purcell et al., 2007) to these called genotypes.

We called genotypes of clones at SNPs based on the raw signal intensities obtained from the Illumina genotyping system.

IBS kinship matrix was calculated based on SNPs called in all analyzed genotypes using the same package.

We called genotypes according to common practice, applying fixed cut-off rules based on read counts [ 18] with ad-hoc R scripts.

All calculations of accuracy below are however done based on raw genotype calls to avoid a bias in favor of either BEAGLE or IMPUTE2.

Based on genotype call cluster separation, cluster variance, and cluster position, variants were assigned to one out of six quality categories (Additional file 2: Figure S2).

The SNP 'call rates' (the proportions of individuals with at least one sequence read at each SNP position) and their minor allele frequencies (MAFs), based on genotype calls, were calculated.

Intensity of each spot on the array following hybridization, washing and scanning along with clustering of data (based on genotype calls of homozygous wild type, heterozygotes and variant homozygous) was assessed.