ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.

ABSTRACT:

Motivation

The development of new high-throughput genotyping products requires a significant investment in testing and training samples to evaluate and optimize the product before it can be used reliably on new samples. One reason for this is current methods for automated calling of genotypes are based on clustering approaches which require a large number of samples to be analyzed simultaneously, or an extensive training dataset to seed clusters. In systems where inbred samples are of primary interest, current clustering approaches perform poorly due to the inability to clearly identify a heterozygote cluster.

Results

As part of the development of two custom single nucleotide polymorphism genotyping products for Oryza sativa (domestic rice), we have developed a new genotype

SUBMITTER: Wright MH 

PROVIDER: S-EPMC2982150 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature