LinkImputeR: user-guided genotype calling and imputation for non-model organisms.

ABSTRACT:

Background

Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and

SUBMITTER: Money D 

PROVIDER: S-EPMC5504746 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature