Sentence examples for quality imputed from inspiring English sources

These criteria were: (1) without any filtering options on SNPs, (2) filtering on the imputation quality of R > 0.8, leaving only the high quality imputed SNPs and (3) filtering with R > 0.8 and MAF > 0.01, additionally excluding alleles with low minor allele frequency.

We identified 209 of the 281 SNPs in the Illumina Omni arrays used for genotyping the DNA samples of the LLFS subjects, while good quality imputed data were available for the other 71 SNPs (mean r2=0.99), and one SNP could not be included in the analysis.

In order to identify duplicate samples that are not annotated as such by ENA we selected the high-quality imputed genotypes.

We were able to recover genotypes at more than 5 million 'high-quality' imputed rare variants, even with the Affymetrix GeneChip 500K Mapping Array Set as a scaffold, which would not be expected to capture variation as well as more recent higher density genotyping products.

We show that the new genotype panel of combined data of exome chip and SNP chip improves imputation quality of imputed rare variants.

There seems to be no consensus yet on the QCs after imputation, and on reporting the quality of imputed genotypes in publications.

Genotype data of both ADNI-1 and ADNI-GO/2 phases were also downloaded, and then quality controlled, imputed, and combined as described in [10].

In this paper, we report a quantitative analysis to assess the quality of imputed genotypes from using both GoNL and 1000G in Dutch and other European populations.

If the quality of imputed genotypes are poor and the pair-wise LD between SNPs calculated by the imputed genotypes is largely different from that by actual genotypes, the estimation of Me using the imputed dataset will be not reliable.

Missing genotypes, due to either low call rates for some SNPs or poor DNA quality, were imputed via random sampling of genotypes with probabilities corresponding to observed genotype frequencies at each locus.

We would expect the quality of imputed rare variants to be improved with more dense GWAS scaffolds, such as the Illumina HumanOmni5-Quad, although this evaluation is beyond the scope of this study.