INTRAPID: A tool for genome wide analysis of interaction between SNPs.

How to get started:

The data needs to be in either a PLINK format or a SNP test format. The appropriate conversion scripts could be downloaded from HERE. A genotype file (file_prefix.geno) and a phenotype file (file_prefix.pheno) would be obtained at this stage.

Commands :

1.  To convert a "ped" and "map" format file (from "PLINK") into an "Intrapid" format,

  plink2Intrapid -ped ped_file_name -map map_file_name

 (SNPtest2Intrapid in case of a SNPtest format file)

     The output files created at this stage would be file_prefix.geno and file_prefix.pheno.

2.  RUN Stage 1 of Rapid Interaction.

     In the sample files, there are 10 SNPs and 1900 individuals. To conduct a "rapid-interaction" for all possible SNPs use,

  CCIntrapid1block -geno geno_file_name -pheno pheno_file_name -regYN 1 -aRapid 0.0001 -range 0 10

     ( QTIntrapid1block for quantitative trait)

     To conduct all possible interactions between two different blocks of SNPs try, (SNPs 0-2 and 8-10 or 2x2 = 4 interactions in this case)

  CCIntrapid2block -geno geno_file_name -pheno pheno_file_name -regYN 1 -aRapid 0.0001 -range 0 2 8 10

    ( QTIntrapid2block for quantitative trait)

    Note: The algorithm is slightly different depending on the nature of analysis that you intend to perform.

    In order to run the program in parallel in multiple cores, one could simply use BASH commands HERE to generate appropriate scripts. The

    "submit_pbs_scripts.sh" script submits jobs to a parallel computing platform, if you had access to one :).