I'm using the PLINK Input Report Plug-in v2.1.3 to import data to PLINK. When I'm adding a Pedigree File Format (Tab-Delimited) into the PedigreeFile section, the plugin does not generate a PED.file. Thus, we only have a .map, .pheno and .script. and PLINK return a error message because it does not find the file. In contrast, using the default parameters, the illumina plugin generate the PED.file. and also the map, .pheno and .script. Since if I don't include the Pedigree File Format, I cannot classify cases as "affected" or "not affected", How I can add this phenotype information when the default values in the Illumina plugin are using?
Thanks in advance