Problem merging data in plink

Problem merging data in plink


welcome everybody…

In short, this is the error message that appears:

Error: 4 variants with 3+ alleles present.

  • If you believe this is due to strand inconsistency, try –flip with
    (Warning: if this seems to work, strand errors involving SNPs with A/T or C/G
    alleles probably remain in your data. If LD between nearby SNPs is high,
    –flip-scan should detect them.)
  • If you are dealing with genuine multiallelic variants, we recommend exporting
    that subset of the data to VCF (via e.g. ‘–recode vcf’), merging with
    another tool/script, and then importing the result; PLINK is not yet suited
    to handling them.
    See for more discussion.

And for the record, I tried to merge this data into EIGENSOFT, but unfortunately the merge also failed and I was getting this message:

*** warning. genetic distances are in cM not Morgans

1 rs1909067 100.026 73942599 T C

Finally this is the command I used in plink:

./plink –bfile data1 –bmerge data2 –make-bed –out merge

I hope to find a solution to my problem.. Thanks in advance



1 hour ago by




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