How to solve the SNP data merge error - TOP and FORWARD allele coding

Solution for the problem when merging two data sets, one with TOP and the other with FORWARD coding. The error message which is displayed is: "...variants with 3+ alleles present." in #PLINK
SNPchiMp website: webserver.ibba...
Data from the video: github.com/Gen...
#rstats script from the video: github.com/Gen...
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[@georgewanjala4605]

Very useful , thanks so much.
What if the merging is successful and then the genotyping rate decreases to even below 50%, what could be the remedy for this?
Thanks in advance

[@GenomicsBootCamp]

Hi,
This could happen if the two merged chips contain SNPs that are only partially overlapping.
In this case find the overlap and print the overlapping SNP names to a text file, and then use the --extract option of PLINK. It is less SNPs, but the individuals will not be deleted unnecessarily by the quality control.
This approach is valid for any merging of unmarching SNP chips, btw.