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Update to Table S2: Timings for Mendel dramatically improved in version 14.2+

Posted by heathercordell on 16 Sep 2014 at 12:16 GMT

In our article "Comparison of Methods to Account for Relatedness in Genome-Wide Association Studies with Family-Based Data", we compare many software packages, in particular those using linear mixed models (LMMs). This type of comparison must be considered a snapshot of a particular point in time, as software packages inevitably evolve. However, a new version of the Mendel package came out as this article was in press that makes such a dramatic difference in its performance, that we felt it deserved an additional short note.

This new version of Mendel (v14.2+) uses theoretical or estimated kinships in its calculations without any of the pre-processing steps mentioned in the paper, considerably improving its ease of use. Moreover, it is now much faster. In Table S2 of our article, Mendel's total analysis time using estimated kinships was listed as 2 hours, 27 minutes and 2 seconds. It now takes 6 minutes and 38 seconds on the same machine, more than 20 times faster, making Mendel now the fastest program.

Of course Mendel's results remain the same. As reported in the paper, all the LMM methods produce essentially the same results with respect to p-values and significant loci recovered.

No competing interests declared.