Simple Question About .Ped Format For Gatk And Plink

Question

[el2622]

The documentation states that in a pedigree file, the first column is family ID, second is pro band ID, third is father ID, and fourth is mother ID. But what is actually separating the ID numbers?

For example, lets say that I have these samples: proband = 1000 father = 1000-01 mother = 1000-02

In this case, would the family ID be 1000? This would mean the pro band ID would be 0? and would the father ID be 01 or would it be -01?

Thanks so much for your help.

Answer 1

[jxchong]

the delimiter is spaces or tabs. This link will help: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped

In particular:

The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:

 Family ID
 Individual ID
 Paternal ID
 Maternal ID
 Sex (1=male; 2=female; other=unknown)
 Phenotype

You have to convert your sample IDs to ped format. What I would do is:

1000 0 01 02 -9 -9
1000 01 0 0 1 -9
1000 02 0 0 2 -9

[Matt Shirley]

You will want these on a new line, I think, like so:

1 1000 1001 1002 -9 -9 (assuming we don't know the sex of the proband)
1 1001 0 0 1 -9
1 1002 0 0 2 -9