Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle
The impact of pedigree information and SNP location determined from either the UMD3.1 genome sequence assembly or the USDA-AIPL map on phasing accuracy were evaluated for 2 chromosomes in 2,778 parent verified Angus sire/offspring pairs. DAGPHASE (Druet and Georges, 2010), using a single generation pedigree was superior to BEAGLE software (Browning and Browning, 2007) for phasing. Results based on USDA-AIPL map are closer to expectation than those based on UMD3.1, but the difference is not significant. Recombination hotspots weredetected near 4 and 82Mb on BTA14, and near 25Mb on BTA15.
Keywords: ASL R2770
How to Cite:
Weng, Z. & Garrick, D. J. & Saatchi, M. & Schnabel, R. & Taylor, J., (2013) “Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle”, Iowa State University Animal Industry Report 10(1). doi: https://doi.org/10.31274/ans_air-180814-632