Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.

ABSTRACT: Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH, an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to re

SUBMITTER: Therese Navarro A 

PROVIDER: S-EPMC10014611 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature