Can't figure out plink --sample-diff
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8 months ago
curious ▴ 820

I want to determine goneotype concordance between two samples in a plink file:

plink2 --bfile myplink --sample-diff ids=sample1 sample2 --out myplink 

I get this error:

Start time: Wed Apr 10 09:47:30 2024
515881 MiB RAM detected; reserving 257940 MiB for main workspace.
Allocated 108818 MiB successfully, after larger attempt(s) failed.
Using up to 64 threads (change this with --threads).
2 samples (0 females, 0 males, 2 ambiguous; 2 founders) loaded from
myplink .fam.
683788 variants loaded from
myplink .bim.
Note: No phenotype data present.
Error: --sample-diff sample ID 'sample1' not found.

I cat the fam file:

cat myplink.fam

and get this:

sample1 sample1 0 0 0 -9
sample1 sample2 0 0 0 -9

Any ideas are greatly appreciated

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