Merging EIGENSOFT data

Question

[yolek64754]

Hi everyone,

I am trying to merge two EIGENSOFT dataset:

• 1240K from here (version 42.4): contains 6676 individual / 1233013 SNPs
• Human Origins from here (from Lazaridis et al. Nature 2016): contains 2068 individuals / 621799 SNPs

However, when I merge it, using the build in mergeit function of EIGENSOFT package, I end up with a dataset with:

• 8744 individual (6676+ 2068 so it's seems ok) and 621272 SNPs.

So it does seems that by merging it, it took the intersection of my two datasets and not all SNPs position. Do you know if there is a way to go around that or am I missing something ?

Thanks a lot