Problem merging data in plink
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 www.cog-genomics.org/plink/1.9/data#merge3 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
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