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 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.  

'''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 Pack Years, Age of Initiation, and Drinks Per Week, 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.