To facilitate studies of genetic variation and their roles in the molecular mechanism of pig complex traits, we developed the Pig Haplotypes Reference Panel (PHARP, http://alphaindex.zju.edu.cn/PHARP/index.php) database, an integrated and interactive knowledge base of pig genomes and their utilization for imputation.
In the current release, PHARP provides the following:
- 9,244 haplotypes (4,622 individuals, related to 140 pig breeds).
- 42.3 million SNPs of autosomes.
- Web-based analytical tools to phase low-density genotypes (genotyped by commonly used commercial SNP arrays technology such as the Illumina PorcineSNP50 Genotyping BeadChip, the Illumina PorcineSNP60 v2 Genotyping BeadChip, and the GeneSeek GGP Porcine 80K SNP chip) and impute them into high-density genotypes.
We demonstrate its applicability for pig commercial 50K SNP arrays, by accurately imputing 2.6 billion genotypes at a concordance rate value of 0.971 in 81 Large White pigs (~17X sequencing coverage).
Overall, as a comprehensive genomic data resource with an imputation focus, PHARP provides a convenient platform for efficient phasing and imputation to facilitate genomic research of variants and their roles in pig complex traits.