diff --git a/README.md b/README.md index 551a7a969b8748a3b6fb4203ced06d4b022355eb..5abed4484fabb0653caebe4e5fb751cb0a9d68a7 100644 --- a/README.md +++ b/README.md @@ -122,24 +122,18 @@ Running LDMAP ------------- #### +LDMAP is run using the following syntax: -Interaction with the core LDMAP binary, `ldmapper1` is most user friendly through the shell wrapper script `ldmap`. Running `ldmap` brings up the following menu: +`./ldmapper1 [input.tped] [intermediate.txt] [job] [out.ldmap] [out.log] [MAF] [HWE]` - L D M A P - Construction of linkage disequilibrium maps from diplotype data... - VERSION 2.0 November 2014 - - - >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - Enter number to select function - 1 Construct LD map in segments from intermediate file - 2 quit +where -#### - -The wrapper script `ldmap` works by requesting parameters from the user, and writing a small executable job files (`.cp`), which then runs `ldmapper1` with these desired parameters when executed. If automation of processes is desired, the required commands may be entered into a `.cp` file directly. An example `.cp` file may look like: -`./ldmapper1 input.tped int job example.map example.log 0.05 0.001` -where `int` is a temporary file used in LD map generation, `job` is a file containing run parameters (eponymous file included with source code), `example.map` will contain the final LD map, and `example.log` will contain detailed run information, `0.05` is the desired AF cutoff, and `0.001` is the desired HWE cutoff. +`[intermediate.txt]` is an intermediate file that will be created;\ +`[job]` is an existing file containing run parameters (included, does not generally need edits);\ +`[out.ldmap]` will be created and contain the final LD map;\ +`[out.log]` will be created and contain detailed run information;\ +`[MAF]` is the desired minor allele frequency cutoff (suggest 0.05);\ +`[HWE]` is the desired Hardy-Weinberg equilibrium deviation p-value cutoff (Suggest 0.001). Output files ------------