Plink genome flag error: Pedigree graph is cyclic
1
0
Entering edit mode
2.2 years ago

I'm using plink 1.9 and running the command:

plink --bfile data --genome --extract data.prune.in --remove data.fail_imiss

where data.fail_imiss is a file with individuals with proportions of missing SNPs greater than greater than the threshold .05 . I get the warnings:

Warning: 10745 het. haploid genotypes present (see plink.hh ); many commands
treat these as missing.
Warning: Nonmissing nonmale Y chromosome genotype(s) present; many commands
treat these as missing.

followed by the error message:

Error: Pedigree graph is cyclic.  Check for evidence of time travel abuse in
your cohort.

I have never seen this error message before and I was wondering if anyone could help me figure it out.

plink • 730 views
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4
Entering edit mode
2.2 years ago

The "pedigree graph" is formed from the father/mother fields in your .fam file. "Pedigree graph is cyclic" means that, according to your .fam file, someone is their own ancestor.

In other words, something went very wrong when the .fam file was created, and you need to backtrack and fix the problem before trying --genome again.

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