Practical Haplotype Graph from Katie Jordon with 472 accessions aligned to Wheat CS RefSeq v2.1
The PHG database was created using PHG v0.35 software then updated to PHG v0.40 using Liquibase plugin. The PHG database was used to impute genotypes from 9K and 90K Illumina to high density (2.9M markers).
- List of scripts use with the PHG
- Align Illumina Infinium data to reference
- Imputation protocol
- Imputation accuracy
- Imputation accuracy by market class
- Breedbase Loading from PHG
- The imputed genotypes can be loaded as a SNP VCF file. The SNP VCF files are large so I have only made them avaialable as links from the Wizard or on the FTP site. Generating SNP VCF
- The haplotypes can also be loaded as a haplotype VCF file. The haplotype VCF can be generated using the following script. Generating haplotype VCF
- Breedbase Integration using wizard
- requires logon account (available to public)
- Select genotyping protocol then genotyping project. If the project has been imputed then expand section "Imputed Genotype Data available", then select "Download File"
- Breedbase FTP site
- look for section labeled "Imputed Protocols"
- Imputation on demand from PHG
- GWAS Analysis
- GWAS on raw data
- GWAS on imputed data
- combine GWAS results using z-value for identical markers
- BrAPI access to PHG
- docker container for accessing genotype information through Breeding API
- R script access to PHG
- R package for accessing th Practical Haplotype Graph, requires Java JDK and rJava
- TASSEL access to PHG
- access to allow building and viewing the PHG graph