In some cases it may be convenient to provide genotypes (and corresponding phenotypes) in multiple files. For example, in a genome-wide study, it may be helpful to have one genotype file containing the HapMap data, and a second genotype file containing the study data. Or, in a candidate gene study where resequencing data are available for a panel of individuals as well as tag-SNP data are available for a study sample, it may be convenient to provide one genotype file for the panel and a second for the tag-SNP data. BIMBAM allows for this use of multiple input files. When using multiple genotype files BIMBAM does not require that the same SNPs be present in both files (although if the same SNP is present in both files then the SNP identifier should be the same in both files, to convey this information). However, to allow for this flexibility, when using multiple genotype files a SNP location file must be provided to specify the locations of the SNPs.
When using multiple genotype files, the user must also provide multiple phenotype files, with each phenotype file corresponding to the individuals in a genotype file. The exception to this is that, if all the individuals in a genotype file have no phenotype data available (as might be the case if the genotypes are from the HapMap individuals for example) then this can be specified using -p 0. The phenotype files must be specified in the same order as the genotype files to which they correspond.