Dear colleagues,I'm using the second version (V2) of Snptest software. Starting from imputed snps obtained from Impute2 analysis (80.000 imputed snps starting from 1071), I have changed the -total_prob_limit parameter in a range from 0.001 to 1 paired with -method score and -method em respectively. No differences in the output files sum up. Impute2 output corresponds to region 2q35 using hg19 human genome. Out of about 80.000 snps ranging in that region, more than a half have not a related p-value. Is in your experience a recurrent issue? Is the fraction of discarded snps too high?
Many thanks,
To unsubscribe from the list visit this webpage 
