Import Data

The Import Data dialog is used to provide information on which map and genotype data files should be used to import a data set into Flapjack.

The map file should contain information on the markers, the chromosome they are on, and their position within that chromosome. The markers do not need to be in any particular order as Flapjack will group and sort them by chromosome and distance once they are loaded. A short example is shown below:

  Marker1      1H     32.5
  Marker2      1H     45.0
  Marker3      2H     23.9

The genotype file should contain a list of variety lines, with allele data per marker for that line. It also requires a header line specifying the marker information for each column.

               Marker1   Marker2   Marker3
  Line1        A         G         G
  Line2        A         -         G/T
  Line3        T         A         C

Both the map file and the genotype file must be in plain-text, tab-delimited format.

Additional import options are available to control the way that Flapjack will read the provided file:

Don't distinguish between heterozygous alleles
Select this option to ensure that duplicate heterozygous alleles are replaced while importing the genotypes. For example, all instances of T/A would be replaced by A/T (or vice versa), so that the final data only contains A/T alleles.
Expect heterozygotes to be separated by a string
This tells Flapjack to look for heterozygotes that are separated by a specific character (defined below). If your data is of the form A/T then this should be used, however, if the data defines AT as a heterozygote then this option should be deselected.
Heterozygous separator string
This specifies the string that is used to define heterozygous alleles within the data.
Missing data string
This specifies the string that is used to define missing genotype data. It can be left blank if no character is used within the genotype file.

Flapjack will display the progress of the import operation as the data is read from the files: