pedigree file

A pedigree, or .ped file indicates relationships among samples. It should be tab-delimited with the following columns in order:

1. family_id -- an identifier that groups samples from the same family
2. sample_id -- a unique id that matches the column in the VCF
3. paternal_id -- either '.' or empty or and id that indicates the sample_id of the father
4. maternal_id -- either '.' or empty or and id that indicates the sample_id of the mother
5. sex -- 1 or male for male samples; 2 or female for female samples or other/unknown/./-9)
6. phenotype -- "affected" , "unaffected" or "1" for unaffected and "2" for affected.

To group kids with the same parents who are not present in the VCF (or the ped), it's possible to simply give them the same (manufactured) parental ids in the appropriate columns.