Changes

The meta-analysis step (stage 2) requires a very specific set of summary statistics, which includes single-variant test statistics and p-values, as well as the test statistic covariance matrix within a sliding window (default: 1Mb). Shuang Feng, Dajiang Liu, and Goncalo Abecasis at the University of Michigan have developed software specifically for this purpose, called Rare-Metal-Worker.  Software and usage instructions to generate necessary single variant statistics is available at [http://genome.sph.umich.edu/wiki/Rare-Metal-Worker  Rare-Metal-Worker].If there are installation problems please let Scott know.

The meta-analysis step (stage 2) requires a very specific set of summary statistics, which includes single-variant test statistics and p-values, as well as the test statistic covariance matrix within a sliding window (default: 1Mb). Shuang Feng, Dajiang Liu, and Goncalo Abecasis at the University of Michigan have developed software specifically for this purpose, called Rare-Metal-Worker.  Software and usage instructions to generate necessary single variant statistics is available at [http://genome.sph.umich.edu/wiki/Rare-Metal-Worker  Rare-Metal-Worker].If there are installation problems please let Scott know.

'''NOTE:''' It is essential that analysis proceeds in the following order. For CPD, please bin quantitative responses and correct for covariates to obtain residuals. For all other phenotypes, please left-anchor responses at 1, log-transform, and then correct for covariates. In this way we will obtain residualized phenotypes ready for analysis with Rare-Metal-Worker. These steps are probably easier to do in your software of choice.  

'''NOTE:''' It is essential that analysis proceeds in the following order. For CPD, please bin quantitative responses and correct for covariates to obtain residuals. For all other phenotypes, please left-anchor responses at 1, log-transform, and then correct for covariates to obtain residuals. In this way we will obtain residualized phenotypes ready for analysis with Rare-Metal-Worker. These steps are probably easier to do in your software of choice.  

Now, using the residualized phenotypes in a .ped file please specify the --makeResiduals and --inverseNormalize options. These will correct for the intercept and then inverse-normalize the phenotype prior to conducting association tests.

Now, using the residualized phenotypes in a .ped file please specify the --makeResiduals and --inverseNormalize options. These will correct for the intercept and then inverse-normalize the phenotype prior to conducting association tests.