Pedigree InformationΒΆ

Flapjack now supports the following pedigree extensions to its genotype file option, which can be imported by including the appropriate headers at the top of a genotype file.


All header lines to Flapjack files begin with #

The headers should be a tab-separated list of columns, in the following format (# fjPedigree is only space separated):

# fjPedigree     <progeny>     <parent-type>     <list of parents of this type>

Parent type can currently be one of:

RP       (recurrent parent)
DP       (donor parent)
N/A      (not applicable)

The <progeny> field can either be a specific progeny name, or the special case of *, meaning that this entry applies to all lines in the dataset (a line will never be assigned itself as a parent though). Multiple instances of the same progeny or parent (by name) will be mapped to all instances of that line name.

For example:

# fjFile = GENOTYPE
# fjPedigree     *       RP     rpParent
# fjPedigree     line1   DP     dpParent1     dpParent2     dpParent3
# fjPedigree     line2   DP     dpParent1
# fjPedigree     line3   N/A    rndParent1    rndParent2
# fjPedigree     line4   N/A    rndParent1    rndParent2
                 mrkr1   mrkr2  mrkr3
line1            A/T     C      T
line2            G       G/A    C
line3            G       G/A    A
line4            A/T     C      T
rpParent         A/T     C      T