Evaluation of variant identification methods for whole genome sequencing data in dairy cattle

The authors thank 2 anonymous reviewers whose comments and suggestions improved this manuscript considerably. C. Baes thanks M. Berner for excellent technical support, P. von Rohr and U. Schuler for fruitful discussions and critical comments on the manuscript and A. Rimmer and D. Bickhart for very insightful thoughts on variant identification methods. We would like to thank the developers of all methods compared in this paper for making their software available. Financial support from the Swiss Commission for Technology and Innovation and the Swiss Cattle Breeders Federation is gratefully acknowledged. S. Jansen was supported by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr “Synbreed –Synergistic plant and animal breeding” (FKZ: 0315528A). This research was partially computed on the HPC equipment at Iowa State University (NSF MRI grant number CNS 1229081, NSF CRI grant number 1205413).