Convert SINGAPORE GENOME VARIATION PROJECT (SGVP) to PLINK format

[manlalayag]

Hello,
I've been trying to convert the SGVP to PLINK format and have not been successful.

SGVP data is available for download here:

http://www.statgen.nus.edu.sg/~SGVP/download.html

I'm a newbie with BASH scripting but I have been able to convert the data to PLINK but when I ran Admixture SGVP with HGDP and 1000Genomes samples, the SGVP is turning up as unique populations.

I can share the code I used but it's too long to post or I can even share the PLINK files but the best help I think I can get is if someone who had successfully converted the samples to PLINK, if you can share one or two of the sample population so I can compare that to what I have done. This way I could know what happened to my conversion script.

I think the script shifts some of the data causing an "alien" like SNPs and creating its unique population.

Thanks in advance.