Changes

=== Stage 1: Local Sites Produce Summary Statistics Using Rare-Metal-Worker ===

=== Stage 1: Local Sites Produce Summary Statistics Using Rare-Metal-Worker ===

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, after each trait has been log-transformed (except for CPD) and corrected for covariates, the residuals are inverse normalized, and then association testing is conducted, in that order.  The Rare-Metal-Worker software has this functionality when you jointly specify

'''NOTE:''' It is essential that, after each trait has been log-transformed (except for CPD) and corrected for covariates, the residuals are inverse normalized, and then association testing is conducted, in that order.  The Rare-Metal-Worker software has this functionality when you jointly specify