PLINK: Whole genome data analysis toolset plink-o-matic...

Some basic information first...


What type of input data do you wish to use? The default is the standard text, white-spaced-delimited (tab and/or space) PED and MAP files. The required format for PED and MAP files is described in the main PLINK website. Binary filesets are compressed to load faster and require less disk space. You can convert a PED/MAP into a binary fileset by selecting the Create binary fileset data management option on the next page (but still select PED/MAP file on this page).

      Standard text-based PED/MAP fileset
      Binary BED/BIM/FAM fileset
      Default single phenotype
      Alternate phenotype fileset


Define filters to exclude SNPs and/or individuals? Second, please indicate whether you will wish to include all SNPs and all individuals in whatever procedure you next select, or if you want the option to impose a set of filters based on factors such as allele frequency and missing genotype rate.

      Do not define SNP or individual filtering thresholds
      Define SNP and/or individual filtering thresholds