qctool v2
A tool for quality control and analysis of gwas datasets.

Converting genotypes

Computing genotype calls by thresholding
The -threshold option tells QCTOOL to compute thresholded genotype calls from genotype probabilities found in the input. For example:
$ qctool -g input.gen -threshold 0.9 -og thresholded.vcf
This will read genotype probabilities (e.g. from imputation) from the input file, and for each sample at each variant will compute a genotype call (if one of the probabilities is above the threshold) or a missing call (if none are).
In the example above, the output VCF file will contain two FORMAT fields, namely GT (the threshholded call) and GP (the original imputed probabilities). More generally, -threshold makes the thresholded call the primary analysis genotype, thus for example in the command:
$ qctool -g input.gen -threshold 0.9 -snp-stats -osnp <output file>
the output will reflect summary statistics computed on the thresholded calls.