Entering edit mode
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
id-delim=' ' ?
( https://groups.google.com/g/plink2-users/c/eIg6ZcWGYCo )
I ended up solving it by setting FID to 0
https://groups.google.com/g/plink2-users/c/1EpoYNRuhMk/m/87Bl1XZqAgAJ