I am merging two datasets. I used "--flip" and could merge almost all chromosomes except for some chromosomes. One of the examples is as below.
Bim file in my dataset1 1 rs2169610 0 103099201 T A Bim file in my dataset2 1 rs2169610 0 103326613 C A
So I think that this is an error due to multiallelic variant. The error message said that PLINK is not yet suited to handling them. So anybody know how to handle this??? Thank you in advance!!!
Error: 1 variant with 3+ alleles present.
* If you believe this is due to strand inconsistency, try --flip with Myfile_Chr1-merge.missnp. (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.