I ran MDS plots on a data set of >620,000 SNPs and 934 individuals using plink.
I followed the advice of a former labmember as well as this tutorial (https://www.staff.ncl.ac.uk/heather.cordell/pak2010MDS.html - mainly just the stuff after "To perform MDS analysis in PLINK, we first calculate a file").
plink --file dataset --genome --out dataset plink --file dataset --read-genome dataset --mds-plot $k --out "dataset_"$k
($k is looped in and is the number of MDS dimensions ranging from 1 to 20).
The first line (genome file creation) does take a while, but I have noticed that the actual mds generation takes about 10 minutes per run and uses about half a gigabyte of RAM, which seems suspiciously quick and non-intensive.
Anyone have any experience with this? (i.e., am I doing something wrong, or is this normal)