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For a solution see
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5050516
The last column can have the following values:
0 – no information have been provided for this individual
1 – only the genotypic data can be used
2 – both the genotypic and phenotypic data can be used
3,4 – The genotypic data can be used. The individual has been initially choosed for the clustering procedure but wasn't included in any sub-group using the given parameters (-> residuals) - and was included in the family by the pedigree reconstruction step. The user can decide whether use also the phenotypic information in one of the sub-groups where he/she appears.
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Saved file after pedigree reconstructon step
#########
1 2757 0 0 2 2
1 2821 0 0 1 1
1 2957 2821 2757 2 2
#########
fam ID father mother sex last column (see above)/splitting status
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My output file (using your sample.ped file) is made up by 8 columns:
1 347 10527 10526 2 1 1 2
1 1092 0 0 2 0 0 1
1 1149 10527 10526 1 1 1 2
1 1557 10527 10526 2 1 1 2
1 2327 8823 8824 2 1 1 2
1 7251 0 0 2 0 0 0
1 7839 8493 8494 1 0 0 1
1 8493 0 0 1 0 0 1
1 8494 8823 8824 2 1 1 2
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hmmm, I tested Jenti 2008.41 with the same data and I'm getting only files with 6 columns...
Which version are you using?
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