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SNP Identification comparison checking

Project start date: 01 March 2013
Project end date: 28 June 2013
Publication date: 28 June 2013
Project status: Completed
Livestock species: Sheep, Goat, Lamb, Grassfed cattle, Grainfed cattle

Summary

This project assessed the commercially available bovine Illumina 50K, HD bovine SNP chips and the Affymetrix HD bovine SNP chip to understand initial infringement profiles. Two approaches were undertaken: 1) Mapping to the bovine genome; and 2) Direct alignment. These two methods minimised potetial problems caused by mismatches and indels between the different sequences, which would lead to ambiguities in the exact position of the SNP's, and to identify adjacent SNP's, and to allow internal validation of the results.