Impact of population stratification and platform bias. Numbers of false positives with and without masking. (A) Effect of population stratification. (B) Effect of heterogeneous platform and variant calling procedures. (Red line) Number of false positives without masking; (blue line) after masking. Note that although masking has little effect on population stratification, it has a much larger impact on platform bias. This is an important behavior: Population stratification introduces real, but confounding signals into disease gene searches; these signals are unaffected by masking (A); in contrast, VAAST's masking option removes false positives due to noise introduced by systematic errors in platform and variant calling procedures (B).
