Low stringency vs. high stringency SNP call validation effectiveness. Validation efficiencies cannot be determined using existing validated SNP data sets, as only 777 SNPs are currently available for rhesus macaque in dbSNP, most of which are polymorphic between subspecies (Chinese to Indian) rather than within subspecies (ie: Indian to Indian). We observed improved validation efficiency using low-stringency SNP calls rather than high-stringency. Both high and low stringency SNP calls were obtained for the reference animal (17573) mate-pair sequence data. The percentage of total SNPs validated in the low-stringency SNP set was slightly less (33.8%) than that observed in the high stringency SNP set (45.7%). In absolute numbers, however, there were 1.8X more SNPs validated from the low stringency SNP calls compared to the high stringency SNP calls.
Fawcett et al. BMC Genomics 2011 12:311 doi:10.1186/1471-2164-12-311