T3/Wheat Practical Haplotype Graph (PHG) imputation

PHG Description

The Practical Haplotype Graph (PHG) V2 database was constructed using whole-exome capture sequencing data from a diverse set of 472 wheat accessions with 2.89M markers
Publication for PHG V1: Development of the Wheat Practical Haplotype Graph
Visualize reference ranges and haplotype counts: JBrowse
Accessions used to create PHG: PHG472_T3Matches.xlsx

Imputation Pipeline

The imputation was done using the ImputePipelinePlugin of the PHG (PHG Wiki). The ImputePipelinePlugin was run with minRead=0 so that all haplotypes are imputed. PHG Version 0.0.40 was used to run the ImputePipelinePlugin.

Imputation accuracy

Genotyping ProtocolPHG accessionOther accessions
Infinium 90K 95% 88%
Infinium 9K 94% 88%
Genotyping by multiplexed sequencing (GMS) 89%

PHG imputation protocol