A framework for the estimation of the proportion of true discoveries in single nucleotide variant detection studies for human data

Any single nucleotide variant detection study could benefit from a fast and cheap method of measuring the quality of variant call list. It is advantageous to be able to see how the call list quality is affected by different variant filtering thresholds and other adjustments to the study parameters. Here we look into a possibility of estimating the proportion of true positives in a single nucleotide variant call list for human data. Using whole-exome and whole-genome gold standard data sets for training, we focus on building a generic model that only relies on information available from any variant caller. We assess and compare the performance of different candidate models based on their practical accuracy. We find that the generic model delivers decent accuracy most of the time. Further, we conclude that its performance could be improved substantially by leveraging the variant quality metrics that are specific to each variant calling tool.