This is a test version of Biostars. For the public version, visit https://www.biostars.org.
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?

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 answer

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

Thank you so much this helps a lot.

Log in to answer this question.