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pedcut

Description

A program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size.

References

Liu F1, Kirichenko A, Axenovich TI, van Duijn CM, Aulchenko YS. An approach for cutting large and complex pedigrees for linkage analysis. Eur J Hum Genet. 2008 Jul;16(7):854-60.

To use pedcut, first set the environment using modules. To see the modules available, type

module avail pedcut

To select a module, type

module load pedcut/[ver]

where [ver] is the version of choice.

How to Use

Just pull up a pedigree file and type pedcut:

$ pedcut -p basic2.ped -m 4 -o basic2_o

	#############################
	#  PedCut version 1.19      #
	#  Fan Liu                  #
	#  Erasmus MC Rotterdam     #
	#############################

Following arguments are under consideration:
--pedin         basic2.ped
--maxbit        4
--out           basic2_o

Start 14:07:54-2015/06/29

Computing pair-wise kinship for 6 Subjects Of Interest (SOI) ...	Done
Forming Rij Matrix ...	Done

Recursion 1 ==> analyzing 17 sub-groups of 6 SOI
progress	0%
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Selected subpedigree 1 ==>	Bit 3	N SOI 6
Done

Recursion complete!

Selected in total 1 sub pedigrees
Created Output basic2_o
Created Output PedsSummary.csv

Finish 14:07:55-2015/06/29
Documentation