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PLINK 1.9 mendel errors trios

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!

plink mendelian error
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updated by chrchang523 chrchang523 • written by Wietje Wietje

1 answer

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.

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written by chrchang523 chrchang523

Thanks a lot, that did the trick!

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written by Wietje Wietje

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