CAPG: comprehensive allopolyploid genotyper.

ABSTRACT:

Motivation

Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heterozygosity, parental cross or other information to resolve read assignment, but good subgenomic references offer the most direct information. The typical strategy aligns reads to the joint reference, performs diploid genotyping within each subgenome, and filters the results, but persistent read misassignment results in an excess of false heterozygous calls.

Results

We introduce the Comprehensive Allopolyploid Genotyper (CAPG), which

SUBMITTER: Kulkarni R 

PROVIDER: S-EPMC9825759 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature