Majority vote and other problems when using computational tools

Computational tools are essential for most of our research. To use these tools, one needs to know how they work. Problems in application of computational methods to variation analysis can appear at several stages and affect, for example, the interpretation of results. Such cases are discussed along with suggestions how to avoid them. The applications include incomplete reporting of methods, especially about the use of prediction tools; method selection on unscientific grounds and without consulting independent method performance assessments; extending application area of methods outside their intended purpose; use of the same data several times for obtaining majority vote; and filtering of datasets so that variants of interest are excluded. All these issues can be avoided by discontinuing the use software tools as black boxes.