I wanted to use the program GERMLINE for the inference of IBD patterns and then DASH for the analysis (http://www1.cs.columbia.edu/~gusev/germline/). GERMLINE accepts PLINK input (.ped and .map) but the manual says that
Although the PLINK format is not intended for haplotypes, GERMLINE expects the respective alleles to appear in order; i.e. the first allele always corresponds to one haplotype and the second allele to the other. Also, PLINK arbitrarily re-orders the alleles in processing the files, so we do not recommend handling phased data with PLINK prior to GERMLINE analysis because the haplotypes may not be intact (use the -from_snp and -to_snp flags to target specific regions).
I have SNP array data in PLINK - do I have to do anything with them before running GERMLINE - or would I need to 'bin' different SNPs into an haplotype ?