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diff --git a/doc/manual.pdf b/doc/manual.pdf index 1b7dc5d..0980ea6 100644 --- a/doc/manual.pdf +++ b/doc/manual.pdf Binary files differdiff --git a/doc/manual.tex b/doc/manual.tex index 73acb60..1cf0400 100644 --- a/doc/manual.tex +++ b/doc/manual.tex @@ -733,21 +733,24 @@ The are a few SNP filters implemented in the software. \item Missingness. By default, SNPs with missingness below 5\% will not be included in the analysis. Use ``-miss [num]'' to change. For - example, ``-miss 0.1'' changes the threshold to 10\%. + example, ``-miss 0.1'' changes the threshold to 10\%. With + ``-miss 1.0'' the filter is disabled. \item Minor allele frequency. By default, SNPs with minor allele frequency below 1\% will not be included in the analysis. Use ``-maf [num]" to change. For example, ``-maf 0.05'' changes the threshold - to 5\%. + to 5\%. With ``-notsnp'' the filter is disabled. \item Correlation with any covariate. By default, SNPs with $r^2$ correlation with any of the covariates above 0.9999 will not be included in the analysis. Use ``-r2 [num]'' to change. For example, - ``-r2 0.999999'' changes the threshold to 0.999999. + ``-r2 0.999999'' changes the threshold to 0.999999. With ``-r2 + 1.0'' the filter is disabled. \item Hardy-Weinberg equilibrium. Use ``-hwe [num]'' to specify. For example, ``-hwe 0.001'' will filter out SNPs with Hardy-Weinberg $p$ - values below 0.001. + values below 0.001. With ``-hwe 0'' or ``--notsnp'' the filter is + disabled. \item User-defined SNP list. Use ``-snps [filename]'' to specify a list of SNPs to be included in the analysis. @@ -1452,7 +1455,7 @@ You can use -outdir with gemma as a bash script \end{verbatim} makes a unique temp directory where the output is stored, here -relative to $HOME, but you can take any path. +relative to \$HOME, but you can take any path. \subsection{How do I prepare the phenotype file for BSLMM?} @@ -1480,8 +1483,6 @@ prefix.prdt.txt file will match the total sample size. Please refer to the GWAS sample data set and some demo scripts included with the GEMMA source code for detailed examples. -\end{enumerate} - \clearpage \newpage |