imbie intersnp uni


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Usage

INTERSNP is written in C/C++ and can be operated from the command line.

 

Compile: g++ intersnp.cpp -o intersnp -lm -O3.

Compile parallel version: g++ intersnp.cpp -o intersnpParallel -lm -O3 -fopenmp

Modification of the source code is necessary for compiling a parallel version!
There are two main loops which can be parallelized in INTERSNP. In order to parallelize the n-loop used for MC-simulations, in particular pathway association analysis, change "#define PARALLELN 0" to "#define PARALLELN 1". To do a full Genome-wide interaction analysis (GWIA) it is recommended to parallelize the A-loop, change "#define PARALLELA 0" to "#define PARALLELA 1".

Run: ./intersnp selectionfile.txt

Run parallel version: ./intersnpParallel selectionfile.txt

 

Howto

Some examples with selectionfiles

Case-Only-Analysis