PLINK 1.9 mendel errors trios

Question

[Wietje]

Hello biostars!

I have a ped-file that contains pedigree information for most of my sample animals and would like to check for mendelian errors but for some reason PLINK (version 1.9) does not recognize duos or trios at all. The set contains full and half sibs and for now my family ID is identical to the individual ID.

Has anyone experienced a similar problem or knows a solution? All help is greatly appreciated!

Answer 1

[chrchang523]

Try setting all your family IDs to "0". The paternal/maternal ID columns can only be used to identify duos/trios when family IDs match.

[Wietje]

Thanks a lot, that did the trick!