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

Some basic information first...

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What type of input fileset do you wish to use? The default is the standard text, white-spaced-delimited (tab and/or space) PED and MAP fileset. Alternatively, binary filesets are compressed to load faster and require less disk space. (To create a binary fileset, select Create binary fileset in the Data Management options on the next page.) In both cases, you can choose a phenotype from an alternate file.

      Standard text-based PED/MAP fileset
      Binary BED/BIM/FAM fileset
      Default fileset phenotype
      Use alternate phenotype file

 

Define filters to exclude SNPs and/or individuals? 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, missing genotype rate and/or chromosomal location.

      Do not define SNP or individual filtering thresholds
      Define SNP and/or individual filtering thresholds
      Do not filter SNPs by location
      Filter SNPs by location