related: How to bypass SNPs with identical A1 and A2 alleles in PLINK?
I have a huge dataset in bim/bed/fam format, for many individuals and separated by chromosome. I'm trying to merge the datasets into a single file using Plink 1.9. I'm getting the error message
Error: Identical A1 and A2 alleles on line 215 of imp_chr1.bim.
The bim file line is
1 rs3131984 0 715348 G G
The data is imputed, and I'd like to keep those alleles. Is there any way to do this?
I've also tried to remove them by creating a list and using --exclude, but I'm getting the same error.
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ommegang •
This is a malformed .bim. You should figure out the original cause of the problem and fix that, if possible.
Failing that, can you post the .log file of your failed --exclude attempt? I just verified that the current plink 1.9 and 2.0 builds allow you to exclude variants like this.
Are you sure this is malformed? I thought this could happen when doing imputation?
That's a bug in the imputation tool. The correct .bim would have one of the alleles set to '0'.
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Hi did you figure this out ? I think I am working on the same dataset and cannot figure out how to bypass this error
Thanks