This study provides a benchmark comparison of tools as well as read depths for four commonly used tools for NGS SNP discovery in a crop species without a reference genome sequence. In addition, a large number of SNPs have been identified in chickpea that would be useful for molecular breeding.
Azam, S.; Thakur, V.; Ruperao, P.; Shah, T.; Balaji, J.; Amindala, B.; Farmer, A.D.; Studholme, D.J.; May, G.D.; Edwards, D.; Jones, J.D.; Varshney, R.K. Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. American Journal of Botany (2012) 99 (2) 186-192. [DOI: 10.3732/ajb.1100419]