Open Access Research article

Methods of tagSNP selection and other variables affecting imputation accuracy in swine

Yvonne M Badke1, Ronald O Bates1, Catherine W Ernst1, Clint Schwab3, Justin Fix4, Curtis P Van Tassell5 and Juan P Steibel12*

Author Affiliations

1 Department of Animal Science, Michigan State University, East Lansing, MI, USA

2 Department of Fisheries & Wildlife, Michigan State University, East Lansing, MI, USA

3 The Maschhoffs, Carlyle, IL, USA

4 National Swine Registry, West Lafayette, IN, USA

5 Bovine Functional Genomics Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA

For all author emails, please log on.

BMC Genetics 2013, 14:8  doi:10.1186/1471-2156-14-8

Published: 21 February 2013

Additional files

Additional file 1: Figure S1:

Effect of reference panel size on imputation accuracy of SNP as a function of their MAF. Weighted mean average imputation accuracy (quantified as r2) as a function of MAF depicted for imputation based on haplotype reference panels of increasing size.

Format: JPG Size: 81KB Download file

Open Data

Additional file 2: Figure S2:

Effect of reference panel size on imputation accuracy of SNP as a function of scaled physical location. Weighted mean average imputation accuracy (quantified as IA) as a function of the scaled chromosomal location for imputation based on haplotype reference panels of increasing size.

Format: JPG Size: 76KB Download file

Open Data