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)
<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.
# 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 etc...