Are values from the within-family id column of a plink .fam file supposed to unique within just the family or within the whole dataset?
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5.2 years ago
curious ▴ 820

consider two families like this:

FAMILY     PERSON   FATHER   MOTHER   SEX
fam1    child1   father1  mother1    m
fam1    mother1   unknown  unknown    f
fam1    father1   unknown  unknown    m
fam2    child2   father2  mother2    m
fam2    mother2   unknown  unknown    f
fam2    father2   unknown  unknown    m

should the .fam be option A:

1    1   2  3    1
1    2   0  0    2
1    3   0  0    1
2    1   2  3    1
2    2   0  0    2
2    3   0  0    1

or option b:

1    1   2  3    1
1    2   0  0    2
1    3   0  0    1
2    4   5  6    1
2    5   0  0    2
2    6   0  0    1

I was implementing option A, but am running into issued with the convertf command of EIGENSOFT giving me errors for having duplicated samples

fatalx:
duplicate sample: 1

Any help is greatly appreciated.

plink gwas • 1.3k views
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5.2 years ago
JC 13k

Should be B, individuals should have unique IDs in your pedigree

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Thank you so much this helps a lot.

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